[{"type":"journal_article","publication":"Energy Advances","ddc":["540"],"citation":{"ama":"Gong L, Zhao S, Yu J, et al. Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. <i>Energy Advances</i>. 2024;3(9):2287-2294. doi:<a href=\"https://doi.org/10.1039/d4ya00334a\">10.1039/d4ya00334a</a>","apa":"Gong, L., Zhao, S., Yu, J., Li, J., Arbiol, J., Kallio, T., … Cabot, A. (2024). Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. <i>Energy Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4ya00334a\">https://doi.org/10.1039/d4ya00334a</a>","ieee":"L. Gong <i>et al.</i>, “Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin,” <i>Energy Advances</i>, vol. 3, no. 9. Royal Society of Chemistry, pp. 2287–2294, 2024.","mla":"Gong, Li, et al. “Influence of the Catalyst Surface Chemistry on the Electrochemical Self-Coupling of Biomass-Derived Benzaldehyde into Hydrobenzoin.” <i>Energy Advances</i>, vol. 3, no. 9, Royal Society of Chemistry, 2024, pp. 2287–94, doi:<a href=\"https://doi.org/10.1039/d4ya00334a\">10.1039/d4ya00334a</a>.","short":"L. Gong, S. Zhao, J. Yu, J. Li, J. Arbiol, T. Kallio, M. Calcabrini, P.R. Martínez-Alanis, M. Ibáñez, A. Cabot, Energy Advances 3 (2024) 2287–2294.","chicago":"Gong, Li, Shiling Zhao, Jing Yu, Junshan Li, Jordi Arbiol, Tanja Kallio, Mariano Calcabrini, Paulina R. Martínez-Alanis, Maria Ibáñez, and Andreu Cabot. “Influence of the Catalyst Surface Chemistry on the Electrochemical Self-Coupling of Biomass-Derived Benzaldehyde into Hydrobenzoin.” <i>Energy Advances</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4ya00334a\">https://doi.org/10.1039/d4ya00334a</a>.","ista":"Gong L, Zhao S, Yu J, Li J, Arbiol J, Kallio T, Calcabrini M, Martínez-Alanis PR, Ibáñez M, Cabot A. 2024. Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin. Energy Advances. 3(9), 2287–2294."},"acknowledgement":"L. Gong and J. Yu thank the China Scholarship Council for the scholarship support. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya. The authors thank support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/AEI/10.13039/501100011033/and by “ERDF A way of making Europe”, by the “European Union”. ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. Authors acknowledge the use of instrumentation as well as the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is founding member of e-DREAM.","intvolume":"         3","quality_controlled":"1","page":"2287-2294","author":[{"last_name":"Gong","full_name":"Gong, Li","first_name":"Li"},{"last_name":"Zhao","first_name":"Shiling","full_name":"Zhao, Shiling"},{"first_name":"Jing","full_name":"Yu, Jing","last_name":"Yu"},{"last_name":"Li","full_name":"Li, Junshan","first_name":"Junshan"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"last_name":"Kallio","first_name":"Tanja","full_name":"Kallio, Tanja"},{"orcid":"0000-0003-4566-5877","last_name":"Calcabrini","full_name":"Calcabrini, Mariano","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martínez-Alanis","first_name":"Paulina R.","full_name":"Martínez-Alanis, Paulina R."},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"_id":"17412","doi":"10.1039/d4ya00334a","scopus_import":"1","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/3.0/","DOAJ_listed":"1","title":"Influence of the catalyst surface chemistry on the electrochemical self-coupling of biomass-derived benzaldehyde into hydrobenzoin","volume":3,"file_date_updated":"2025-01-09T12:29:09Z","date_created":"2024-08-11T22:01:12Z","day":"01","abstract":[{"lang":"eng","text":"The electroreduction of biomass-derived benzaldehyde (BZH) provides a potentially cost-effective route to produce benzyl alcohol (BA). This reaction competes with the electrochemical self-coupling of BZH to hydrobenzoin (HDB), which holds significance as a biofuel. Herein, we demonstrate the selectivity towards one or the other product strongly depends on the surface chemistry of the catalyst, specifically on its ability to adsorb hydrogen, as showcased with Cu2S electrocatalysts. We particularly analyze the effect of surface ligands, oleylamine (OAm), on the selective conversion of BZH to BA or HDB. The effect of the electrode potential, electrolyte pH, and temperature are studied. Results indicate that bare Cu2S exhibits higher selectivity towards BA, while OAm-capped Cu2S promotes HDB formation. This difference is explained by the competing adsorption of protons and BZH. During the BZH electrochemical conversion, electrons first transfer to the C in the C[double bond, length as m-dash]O group to form a ketyl radical. Then the radical either couples with surrounding H+ to form BA or self-couple to produce HDB, depending on the H+ availability that is affected by the electrocatalyst surface properties. The presence of OAm inhibits the H adsorption on the electrode surface therefore reducing the formation of high-energy state Had and its combination with ketyl radicals to form BA. Instead, the presence of OAm promotes the outer sphere reaction for obtaining HDB."}],"publication_identifier":{"eissn":["2753-1457"]},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"18812","file_name":"2024_EnergyAdvances_Gong.pdf","date_created":"2025-01-09T12:29:09Z","relation":"main_file","date_updated":"2025-01-09T12:29:09Z","creator":"dernst","file_size":1448762,"content_type":"application/pdf","access_level":"open_access","checksum":"4a49515ec90354d005852e741bff1d29","success":1}],"OA_type":"gold","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"issue":"9","year":"2024","status":"public","has_accepted_license":"1","publication_status":"published","date_updated":"2025-01-09T12:30:16Z","month":"09","article_type":"original","date_published":"2024-09-01T00:00:00Z","publisher":"Royal Society of Chemistry","oa":1,"article_processing_charge":"Yes","department":[{"_id":"MaIb"}]},{"quality_controlled":"1","page":"284-303","author":[{"full_name":"Froleyks, Nils","first_name":"Nils","last_name":"Froleyks"},{"last_name":"Yu","first_name":"Zhengqi","full_name":"Yu, Zhengqi","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342"},{"first_name":"Armin","full_name":"Biere, Armin","last_name":"Biere"},{"last_name":"Heljanko","full_name":"Heljanko, Keijo","first_name":"Keijo"}],"_id":"17413","doi":"10.1007/978-3-031-63498-7_17","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"type":"conference","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","ddc":["000"],"external_id":{"arxiv":["2405.04297"],"isi":["001273489700017"]},"acknowledgement":"This work is supported by the Austrian Science Fund (FWF) under the project W1255-N23, the LIT AI Lab funded by the State of Upper Austria, the ERC-2020-AdG 101020093, the Academy of Finland under the project 336092 and by a gift from Intel Corporation.","citation":{"mla":"Froleyks, Nils, et al. “Certifying Phase Abstraction.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 14739, Springer Nature, 2024, pp. 284–303, doi:<a href=\"https://doi.org/10.1007/978-3-031-63498-7_17\">10.1007/978-3-031-63498-7_17</a>.","ieee":"N. Froleyks, E. Yu, A. Biere, and K. Heljanko, “Certifying phase abstraction,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Nancy, France, 2024, vol. 14739, pp. 284–303.","ama":"Froleyks N, Yu E, Biere A, Heljanko K. Certifying phase abstraction. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 14739. Springer Nature; 2024:284-303. doi:<a href=\"https://doi.org/10.1007/978-3-031-63498-7_17\">10.1007/978-3-031-63498-7_17</a>","apa":"Froleyks, N., Yu, E., Biere, A., &#38; Heljanko, K. (2024). Certifying phase abstraction. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 14739, pp. 284–303). Nancy, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-63498-7_17\">https://doi.org/10.1007/978-3-031-63498-7_17</a>","ista":"Froleyks N, Yu E, Biere A, Heljanko K. 2024. Certifying phase abstraction. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 14739, 284–303.","short":"N. Froleyks, E. Yu, A. Biere, K. Heljanko, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp. 284–303.","chicago":"Froleyks, Nils, Emily Yu, Armin Biere, and Keijo Heljanko. “Certifying Phase Abstraction.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 14739:284–303. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-63498-7_17\">https://doi.org/10.1007/978-3-031-63498-7_17</a>."},"intvolume":"     14739","arxiv":1,"language":[{"iso":"eng"}],"title":"Certifying phase abstraction","volume":14739,"file_date_updated":"2024-08-12T06:53:39Z","date_created":"2024-08-11T22:01:13Z","abstract":[{"lang":"eng","text":"Certification helps to increase trust in formal verification of safety-critical systems which require assurance on their correctness. In hardware model checking, a widely used formal verification technique, phase abstraction is considered one of the most commonly used preprocessing techniques. We present an approach to certify an extended form of phase abstraction using a generic certificate format. As in earlier works our approach involves constructing a witness circuit with an inductive invariant property that certifies the correctness of the entire model checking process, which is then validated by an independent certificate checker. We have implemented and evaluated the proposed approach including certification for various preprocessing configurations on hardware model checking competition benchmarks. As an improvement on previous work in this area, the proposed method is able to efficiently complete certification with an overhead of a fraction of model checking time."}],"day":"01","scopus_import":"1","isi":1,"status":"public","year":"2024","has_accepted_license":"1","publication_identifier":{"isbn":["9783031634970"],"issn":["0302-9743"],"eissn":["1611-3349"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","file":[{"file_id":"17414","file_name":"2024_LNCS_Froleyks.pdf","date_created":"2024-08-12T06:53:39Z","relation":"main_file","date_updated":"2024-08-12T06:53:39Z","creator":"dernst","file_size":556902,"checksum":"7d7839fc8c5c680ea3ac09f40a66e55d","access_level":"open_access","content_type":"application/pdf","success":1}],"alternative_title":["LNCS"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa":1,"article_processing_charge":"Yes (in subscription journal)","conference":{"end_date":"2024-07-06","location":"Nancy, France","start_date":"2024-07-03","name":"IJCAR: International Joint Conference on Automated Reasoning"},"department":[{"_id":"ToHe"}],"publication_status":"published","date_updated":"2025-09-08T08:49:53Z","month":"07","date_published":"2024-07-01T00:00:00Z","publisher":"Springer Nature","ec_funded":1},{"language":[{"iso":"eng"}],"title":"Reach for the arcs: Reconstructing surfaces from SDFs via tangent points","conference":{"location":"Denver, CO, United States","end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-27"},"article_number":"23","date_created":"2024-08-12T10:02:58Z","day":"13","abstract":[{"text":"We introduce an algorithm to reconstruct a mesh from discrete samples of a shape’s Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted with existing techniques. We extract all possible information from the SDF data, outperforming commonly used algorithms and imposing no topological or geometric restrictions.","lang":"eng"}],"article_processing_charge":"No","date_updated":"2024-08-12T10:11:19Z","scopus_import":"1","extern":"1","publication_status":"published","date_published":"2024-07-13T00:00:00Z","month":"07","publisher":"Association for Computing Machinery","author":[{"last_name":"Sellán","first_name":"Silvia","full_name":"Sellán, Silvia"},{"full_name":"Ren, Yingying","first_name":"Yingying","id":"93d68d10-3540-11ef-a265-f748a50dba3d","last_name":"Ren"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"first_name":"Oded","full_name":"Stein, Oded","last_name":"Stein"}],"status":"public","year":"2024","quality_controlled":"1","_id":"17423","doi":"10.1145/3641519.3657419","publication":"SIGGRAPH '24: Special Interest Group on Computer Graphics and Interactive Techniques Conference","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9798400705250"]},"oa_version":"None","citation":{"short":"S. Sellán, Y. Ren, C. Batty, O. Stein, in:, SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference, Association for Computing Machinery, 2024.","chicago":"Sellán, Silvia, Yingying Ren, Christopher Batty, and Oded Stein. “Reach for the Arcs: Reconstructing Surfaces from SDFs via Tangent Points.” In <i>SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657419\">https://doi.org/10.1145/3641519.3657419</a>.","ista":"Sellán S, Ren Y, Batty C, Stein O. 2024. Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 23.","ama":"Sellán S, Ren Y, Batty C, Stein O. Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. In: <i>SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657419\">10.1145/3641519.3657419</a>","apa":"Sellán, S., Ren, Y., Batty, C., &#38; Stein, O. (2024). Reach for the arcs: Reconstructing surfaces from SDFs via tangent points. In <i>SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference</i>. Denver, CO, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657419\">https://doi.org/10.1145/3641519.3657419</a>","ieee":"S. Sellán, Y. Ren, C. Batty, and O. Stein, “Reach for the arcs: Reconstructing surfaces from SDFs via tangent points,” in <i>SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference</i>, Denver, CO, United States, 2024.","mla":"Sellán, Silvia, et al. “Reach for the Arcs: Reconstructing Surfaces from SDFs via Tangent Points.” <i>SIGGRAPH ’24: Special Interest Group on Computer Graphics and Interactive Techniques Conference</i>, 23, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657419\">10.1145/3641519.3657419</a>."}},{"month":"07","article_type":"original","date_published":"2024-07-19T00:00:00Z","date_updated":"2024-08-12T10:08:13Z","publication_status":"published","scopus_import":"1","extern":"1","publisher":"Association for Computing Machinery","title":"Computational homogenization for inverse design of surface-based inflatables","language":[{"iso":"eng"}],"volume":43,"article_processing_charge":"No","day":"19","abstract":[{"lang":"eng","text":"Surface-based inflatables are composed of two thin layers of nearly inextensible sheet material joined together along carefully selected fusing curves. During inflation, pressure forces separate the two sheets to maximize the enclosed volume. The fusing curves restrict this expansion, leading to a spatially varying in-plane contraction and hence metric frustration. The inflated structure settles into a 3D equilibrium that balances pressure forces with the internal elastic forces of the sheets.\r\nWe present a computational framework for analyzing and designing surface-based inflatable structures with arbitrary fusing patterns. Our approach employs numerical homogenization to characterize the behavior of parametric families of periodic inflatable patch geometries, which can then be combined to tessellate the sheet with smoothly varying patterns. We propose a novel parametrization of the underlying deformation space that allows accurate, efficient, and systematical analysis of the stretching and bending behavior of inflated patches with potentially open boundaries.\r\nWe apply our homogenization algorithm to create a database of geometrically diverse fusing patterns spanning a wide range of material properties and deformation characteristics. This database is employed in an inverse design algorithm that solves for fusing curves to best approximate a given input target surface. Local patches are selected and blended to form a global network of curves based on a geometric flattening algorithm. These fusing curves are then further optimized to minimize the distance of the deployed structure to target surface. We show that this approach offers greater flexibility to approximate given target geometries compared to previous work while significantly improving structural performance."}],"date_created":"2024-08-12T10:03:38Z","article_number":"87","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"type":"journal_article","publication":"ACM Transactions on Graphics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ren Y, Panetta J, Suzuki S, Kusupati U, Isvoranu F, Pauly M. 2024. Computational homogenization for inverse design of surface-based inflatables. ACM Transactions on Graphics. 43(4), 87.","short":"Y. Ren, J. Panetta, S. Suzuki, U. Kusupati, F. Isvoranu, M. Pauly, ACM Transactions on Graphics 43 (2024).","chicago":"Ren, Yingying, Julian Panetta, Seiichi Suzuki, Uday Kusupati, Florin Isvoranu, and Mark Pauly. “Computational Homogenization for Inverse Design of Surface-Based Inflatables.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658125\">https://doi.org/10.1145/3658125</a>.","ieee":"Y. Ren, J. Panetta, S. Suzuki, U. Kusupati, F. Isvoranu, and M. Pauly, “Computational homogenization for inverse design of surface-based inflatables,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","mla":"Ren, Yingying, et al. “Computational Homogenization for Inverse Design of Surface-Based Inflatables.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 87, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658125\">10.1145/3658125</a>.","ama":"Ren Y, Panetta J, Suzuki S, Kusupati U, Isvoranu F, Pauly M. Computational homogenization for inverse design of surface-based inflatables. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658125\">10.1145/3658125</a>","apa":"Ren, Y., Panetta, J., Suzuki, S., Kusupati, U., Isvoranu, F., &#38; Pauly, M. (2024). Computational homogenization for inverse design of surface-based inflatables. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658125\">https://doi.org/10.1145/3658125</a>"},"oa_version":"None","intvolume":"        43","quality_controlled":"1","author":[{"last_name":"Ren","id":"93d68d10-3540-11ef-a265-f748a50dba3d","full_name":"Ren, Yingying","first_name":"Yingying"},{"first_name":"Julian","full_name":"Panetta, Julian","last_name":"Panetta"},{"full_name":"Suzuki, Seiichi","first_name":"Seiichi","last_name":"Suzuki"},{"first_name":"Uday","full_name":"Kusupati, Uday","last_name":"Kusupati"},{"first_name":"Florin","full_name":"Isvoranu, Florin","last_name":"Isvoranu"},{"full_name":"Pauly, Mark","first_name":"Mark","last_name":"Pauly"}],"year":"2024","issue":"4","status":"public","doi":"10.1145/3658125","_id":"17424"},{"scopus_import":"1","pmid":1,"volume":2831,"series_title":"MIMB","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","related_material":{"record":[{"relation":"dissertation_contains","id":"20212","status":"public"}]},"language":[{"iso":"eng"}],"day":"13","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"date_created":"2024-08-13T12:16:41Z","place":"New York, NY","publication":"Neuronal Morphogenesis","type":"book_chapter","intvolume":"      2831","citation":{"apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299."},"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","external_id":{"pmid":["39134857"]},"author":[{"full_name":"Miranda, Osvaldo","first_name":"Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","last_name":"Miranda"},{"orcid":"0000-0001-8457-2572","last_name":"Cheung","full_name":"Cheung, Giselle T","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"page":"283-299","quality_controlled":"1","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1007/978-1-0716-3969-6_19","_id":"17425","month":"08","date_published":"2024-08-13T00:00:00Z","publication_status":"published","date_updated":"2026-04-07T12:32:35Z","acknowledged_ssus":[{"_id":"Bio"}],"publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["9781071639696"],"eissn":["1940-6029"],"isbn":["9781071639689"],"issn":["1064-3745"]},"alternative_title":["Methods in Molecular Biology"],"oa_version":"None","year":"2024","status":"public","corr_author":"1","edition":"1","editor":[{"first_name":"Kazuhito","full_name":"Toyooka, Kazuhito","last_name":"Toyooka"}]},{"abstract":[{"text":"The robustness of neural networks against input perturbations with bounded\r\nmagnitude represents a serious concern in the deployment of deep learning\r\nmodels in safety-critical systems. Recently, the scientific community has\r\nfocused on enhancing certifiable robustness guarantees by crafting 1-Lipschitz\r\nneural networks that leverage Lipschitz bounded dense and convolutional layers.\r\nAlthough different methods have been proposed in the literature to achieve this\r\ngoal, understanding the performance of such methods is not straightforward,\r\nsince different metrics can be relevant (e.g., training time, memory usage,\r\naccuracy, certifiable robustness) for different applications. For this reason,\r\nthis work provides a thorough theoretical and empirical comparison between\r\nmethods by evaluating them in terms of memory usage, speed, and certifiable\r\nrobust accuracy. The paper also provides some guidelines and recommendations to\r\nsupport the user in selecting the methods that work best depending on the\r\navailable resources. We provide code at\r\nhttps://github.com/berndprach/1LipschitzLayersCompared.","lang":"eng"}],"day":"01","date_created":"2024-08-14T08:42:32Z","title":"1-Lipschitz layers compared: Memory, speed, and certifiable robustness","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.16833","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19759"}],"link":[{"url":"https://github.com/berndprach/1LipschitzLayersCompared","relation":"software"}]},"language":[{"iso":"eng"}],"isi":1,"doi":"10.1109/CVPR52733.2024.02320","_id":"17426","page":"24574-24583","author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","first_name":"Bernd","last_name":"Prach"},{"full_name":"Brau, Fabio","first_name":"Fabio","last_name":"Brau"},{"first_name":"Giorgio","full_name":"Buttazzo, Giorgio","last_name":"Buttazzo"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"quality_controlled":"1","arxiv":1,"citation":{"ama":"Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Computer Vision Foundation; 2024:24574-24583. doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>","apa":"Prach, B., Brau, F., Buttazzo, G., &#38; Lampert, C. (2024). 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24574–24583). Seattle, WA, United States: Computer Vision Foundation. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>","ieee":"B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared: Memory, speed, and certifiable robustness,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Seattle, WA, United States, 2024, pp. 24574–24583.","mla":"Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Computer Vision Foundation, 2024, pp. 24574–83, doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>.","short":"B. Prach, F. Brau, G. Buttazzo, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–24583.","chicago":"Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24574–83. Computer Vision Foundation, 2024. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>.","ista":"Prach B, Brau F, Buttazzo G, Lampert C. 2024. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24574–24583."},"acknowledgement":"This work was partially supported by project SERICS (PE00000014) under the MUR National Recovery and Resilience Plan funded by the European Union - NextGenerationEU.\r\n","external_id":{"arxiv":["2311.16833"],"isi":["001344387500055"]},"type":"conference","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"conference":{"start_date":"2024-06-16","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2024-06-22","location":"Seattle, WA, United States"},"article_processing_charge":"No","oa":1,"publisher":"Computer Vision Foundation","month":"06","date_published":"2024-06-01T00:00:00Z","date_updated":"2026-04-07T11:49:51Z","publication_status":"published","corr_author":"1","has_accepted_license":"1","year":"2024","status":"public","OA_type":"green","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository"},{"oa":1,"department":[{"_id":"CaMu"}],"article_number":"e2023JD040413","article_processing_charge":"Yes (in subscription journal)","date_published":"2024-08-16T00:00:00Z","article_type":"original","month":"08","date_updated":"2025-09-08T08:56:53Z","publication_status":"published","ec_funded":1,"publisher":"Wiley","issue":"15","year":"2024","status":"public","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]},"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"relation":"main_file","file_name":"2024_JGRAtmospheres_Andre.pdf","date_created":"2024-08-19T06:32:21Z","file_id":"17438","success":1,"creator":"dernst","checksum":"71d7f966318e11ce474737f4e37405ef","file_size":8126046,"access_level":"open_access","content_type":"application/pdf","date_updated":"2024-08-19T06:32:21Z"}],"oa_version":"Published Version","file_date_updated":"2024-08-19T06:32:21Z","volume":129,"title":"Regimes of precipitation change over Europe and the Mediterranean","license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"day":"16","abstract":[{"text":"The Mediterranean region is experiencing pronounced aridification and in certain areas higher occurrence of intense precipitation. In this work, we analyze the evolution of the precipitation probability distribution in terms of precipitating days (or “wet-days”) and all-days quantile trends, in Europe and the Mediterranean, using the ERA5 reanalysis. Looking at the form of wet-days quantile trends curves, we identify four regimes. Two are predominant: in most of northern Europe the precipitation quantiles all intensify, while in the Mediterranean the low-medium quantiles are mostly decreasing as extremes intensify or decrease. The wet-days distribution is then modeled by a Weibull law with two parameters, whose changes capture the four regimes. Assessing the significance of the parameters' changes over 1950–2020 shows that a signal on wet-days distribution has already emerged in northern Europe (where the distribution shifts to more intense precipitation), but not yet in the Mediterranean, where the natural variability is stronger. We extend the results by describing the all-days distribution change as the wet-days’ change plus a contribution from the dry-days frequency change, and study their relative contribution. In northern Europe, the wet-days distribution change is the dominant driver, and the contribution of dry-days frequency change can be neglected for wet-days percentiles above about 50%. In the Mediterranean, however, the change of precipitation distribution comes from the significant increase of dry-days frequency instead of an intensity change during wet-days. Therefore, in the Mediterranean the increase of dry-days frequency is crucial for all-days trends, even for heavy precipitation.","lang":"eng"}],"date_created":"2024-08-18T22:01:04Z","isi":1,"scopus_import":"1","author":[{"full_name":"André, Julie","first_name":"Julie","last_name":"André"},{"last_name":"D'Andrea","first_name":"Fabio","full_name":"D'Andrea, Fabio"},{"full_name":"Drobinski, Philippe","first_name":"Philippe","last_name":"Drobinski"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"805041","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"doi":"10.1029/2023JD040413","_id":"17435","type":"journal_article","publication":"Journal of Geophysical Research: Atmospheres","intvolume":"       129","citation":{"chicago":"André, Julie, Fabio D’Andrea, Philippe Drobinski, and Caroline J Muller. “Regimes of Precipitation Change over Europe and the Mediterranean.” <i>Journal of Geophysical Research: Atmospheres</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023JD040413\">https://doi.org/10.1029/2023JD040413</a>.","short":"J. André, F. D’Andrea, P. Drobinski, C.J. Muller, Journal of Geophysical Research: Atmospheres 129 (2024).","ista":"André J, D’Andrea F, Drobinski P, Muller CJ. 2024. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 129(15), e2023JD040413.","apa":"André, J., D’Andrea, F., Drobinski, P., &#38; Muller, C. J. (2024). Regimes of precipitation change over Europe and the Mediterranean. <i>Journal of Geophysical Research: Atmospheres</i>. Wiley. <a href=\"https://doi.org/10.1029/2023JD040413\">https://doi.org/10.1029/2023JD040413</a>","ama":"André J, D’Andrea F, Drobinski P, Muller CJ. Regimes of precipitation change over Europe and the Mediterranean. <i>Journal of Geophysical Research: Atmospheres</i>. 2024;129(15). doi:<a href=\"https://doi.org/10.1029/2023JD040413\">10.1029/2023JD040413</a>","mla":"André, Julie, et al. “Regimes of Precipitation Change over Europe and the Mediterranean.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 15, e2023JD040413, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023JD040413\">10.1029/2023JD040413</a>.","ieee":"J. André, F. D’Andrea, P. Drobinski, and C. J. Muller, “Regimes of precipitation change over Europe and the Mediterranean,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 15. Wiley, 2024."},"acknowledgement":"CJM gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No 805041). The authors also thank Samuel Somot (Centre National de Recherches Météorologiques, Toulouse) and Juliette Blanchet (Institut des Géosciences de l’Environnement, Grenoble) for their fruitful discussions on the project.","external_id":{"isi":["001285897600001"]},"ddc":["550"]},{"oa_version":"Published Version","file":[{"file_id":"18811","relation":"main_file","file_name":"2024_PlantCommunications_Das.pdf","date_created":"2025-01-09T12:25:32Z","date_updated":"2025-01-09T12:25:32Z","success":1,"creator":"dernst","file_size":4970540,"content_type":"application/pdf","checksum":"38cabc1042ac7fb70e6c4c510eba88fc","access_level":"open_access"}],"OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["2590-3462"]},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","year":"2024","issue":"11","status":"public","publisher":"Elsevier","date_updated":"2025-01-09T12:26:55Z","publication_status":"published","article_type":"original","month":"11","date_published":"2024-11-11T00:00:00Z","article_processing_charge":"Yes","department":[{"_id":"JiFr"}],"article_number":"101039","oa":1,"ddc":["580"],"external_id":{"pmid":["38988072"]},"acknowledgement":"We are grateful to Iris Nieuwland and Neri van Laar for experimental support. No conflict of interest declared.\r\nThis work was supported by the Netherlands Organisation for Scientific Research, the Netherlands (grants ALWOP.402 and OCENW.M20.031 to J.W.B.) and the Human Frontiers Research Program (grant RGP0015/2022 to D.W.).","citation":{"short":"S. Das, M. De Roij, S. Bellows, M.D. Alvarez, S. Mutte, W. Kohlen, E. Farcot, D. Weijers, J.W. Borst, Plant Communications 5 (2024).","chicago":"Das, Shubhajit, Martijn De Roij, Simon Bellows, Melissa Dipp Alvarez, Sumanth Mutte, Wouter Kohlen, Etienne Farcot, Dolf Weijers, and Jan Willem Borst. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>.","ista":"Das S, De Roij M, Bellows S, Alvarez MD, Mutte S, Kohlen W, Farcot E, Weijers D, Borst JW. 2024. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. Plant Communications. 5(11), 101039.","ama":"Das S, De Roij M, Bellows S, et al. Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. 2024;5(11). doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>","apa":"Das, S., De Roij, M., Bellows, S., Alvarez, M. D., Mutte, S., Kohlen, W., … Borst, J. W. (2024). Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">https://doi.org/10.1016/j.xplc.2024.101039</a>","ieee":"S. Das <i>et al.</i>, “Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination,” <i>Plant Communications</i>, vol. 5, no. 11. Elsevier, 2024.","mla":"Das, Shubhajit, et al. “Quantitative Imaging Reveals the Role of MpARF Proteasomal Degradation during Gemma Germination.” <i>Plant Communications</i>, vol. 5, no. 11, 101039, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xplc.2024.101039\">10.1016/j.xplc.2024.101039</a>."},"intvolume":"         5","type":"journal_article","publication":"Plant Communications","_id":"17436","doi":"10.1016/j.xplc.2024.101039","quality_controlled":"1","author":[{"last_name":"Das","full_name":"Das, Shubhajit","first_name":"Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be"},{"full_name":"De Roij, Martijn","first_name":"Martijn","last_name":"De Roij"},{"full_name":"Bellows, Simon","first_name":"Simon","last_name":"Bellows"},{"last_name":"Alvarez","first_name":"Melissa Dipp","full_name":"Alvarez, Melissa Dipp"},{"full_name":"Mutte, Sumanth","first_name":"Sumanth","last_name":"Mutte"},{"first_name":"Wouter","full_name":"Kohlen, Wouter","last_name":"Kohlen"},{"first_name":"Etienne","full_name":"Farcot, Etienne","last_name":"Farcot"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"last_name":"Borst","first_name":"Jan Willem","full_name":"Borst, Jan Willem"}],"pmid":1,"scopus_import":"1","date_created":"2024-08-18T22:01:04Z","abstract":[{"text":"The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination.","lang":"eng"}],"day":"11","language":[{"iso":"eng"}],"DOAJ_listed":"1","title":"Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination","volume":5,"file_date_updated":"2025-01-09T12:25:32Z"},{"doi":"10.1007/s00031-024-09873-0","_id":"17437","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"quality_controlled":"1","author":[{"id":"19f1e3bf-c59a-11ee-a1af-ed269948817b","full_name":"Vernet, Tanguy","first_name":"Tanguy","last_name":"Vernet"}],"citation":{"chicago":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>.","short":"T. Vernet, Transformation Groups (2024).","ista":"Vernet T. 2024. Rational singularities for moment maps of totally negative quivers. Transformation Groups.","apa":"Vernet, T. (2024). Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>","ama":"Vernet T. Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. 2024. doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>","mla":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>.","ieee":"T. Vernet, “Rational singularities for moment maps of totally negative quivers,” <i>Transformation Groups</i>. Springer Nature, 2024."},"acknowledgement":"I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","external_id":{"isi":["001287455300001"]},"ddc":["510"],"type":"journal_article","publication":"Transformation Groups","day":"09","abstract":[{"lang":"eng","text":"We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves."}],"date_created":"2024-08-18T22:01:04Z","title":"Rational singularities for moment maps of totally negative quivers","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s00031-024-09873-0","open_access":"1"}],"scopus_import":"1","isi":1,"has_accepted_license":"1","corr_author":"1","year":"2024","status":"public","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1531-586X"],"issn":["1083-4362"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"TaHa"}],"oa":1,"publisher":"Springer Nature","ec_funded":1,"date_published":"2024-09-09T00:00:00Z","month":"09","article_type":"original","date_updated":"2025-09-08T08:56:08Z","publication_status":"epub_ahead"},{"date_created":"2024-08-19T09:41:18Z","abstract":[{"lang":"eng","text":"Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE–guide–target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.\r\n\r\n"}],"day":"27","volume":630,"main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11649018/"}],"language":[{"iso":"eng"}],"title":"Plasmid targeting and destruction by the DdmDE bacterial defence system","pmid":1,"scopus_import":"1","_id":"17442","doi":"10.1038/s41586-024-07515-9","author":[{"last_name":"Bravo","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly"},{"last_name":"Ramos","full_name":"Ramos, Delisa A.","first_name":"Delisa A."},{"last_name":"Fregoso Ocampo","full_name":"Fregoso Ocampo, Rodrigo","first_name":"Rodrigo"},{"first_name":"Caiden","full_name":"Ingram, Caiden","last_name":"Ingram"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"}],"page":"961-967","quality_controlled":"1","intvolume":"       630","external_id":{"pmid":["38740055"]},"citation":{"ama":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. <i>Nature</i>. 2024;630(8018):961-967. doi:<a href=\"https://doi.org/10.1038/s41586-024-07515-9\">10.1038/s41586-024-07515-9</a>","apa":"Bravo, J. P. K., Ramos, D. A., Fregoso Ocampo, R., Ingram, C., &#38; Taylor, D. W. (2024). Plasmid targeting and destruction by the DdmDE bacterial defence system. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07515-9\">https://doi.org/10.1038/s41586-024-07515-9</a>","ieee":"J. P. K. Bravo, D. A. Ramos, R. Fregoso Ocampo, C. Ingram, and D. W. Taylor, “Plasmid targeting and destruction by the DdmDE bacterial defence system,” <i>Nature</i>, vol. 630, no. 8018. Springer Nature, pp. 961–967, 2024.","mla":"Bravo, Jack Peter Kelly, et al. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” <i>Nature</i>, vol. 630, no. 8018, Springer Nature, 2024, pp. 961–67, doi:<a href=\"https://doi.org/10.1038/s41586-024-07515-9\">10.1038/s41586-024-07515-9</a>.","short":"J.P.K. Bravo, D.A. Ramos, R. Fregoso Ocampo, C. Ingram, D.W. Taylor, Nature 630 (2024) 961–967.","chicago":"Bravo, Jack Peter Kelly, Delisa A. Ramos, Rodrigo Fregoso Ocampo, Caiden Ingram, and David W. Taylor. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07515-9\">https://doi.org/10.1038/s41586-024-07515-9</a>.","ista":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. 2024. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 630(8018), 961–967."},"acknowledgement":"We thank K. Kiernan, G. Hibshman and I. Strohkendl for insightful discussions and comments on the manuscript, and R. Lin for assistance with the ATPase assay. Data were collected at the Sauer Structural Biology Laboratory at the University of Texas at Austin. This work was supported in part by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) R35GM138348 (to D.W.T.) and Welch Foundation research grant F-1938 (to D.W.T.).","type":"journal_article","publication":"Nature","department":[{"_id":"JaBr"}],"article_processing_charge":"No","oa":1,"publisher":"Springer Nature","date_updated":"2025-06-24T12:47:21Z","publication_status":"published","date_published":"2024-06-27T00:00:00Z","article_type":"original","month":"06","corr_author":"1","issue":"8018","year":"2024","status":"public","OA_type":"green","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"OA_place":"repository"},{"ec_funded":1,"publisher":"Wiley","publication_status":"published","date_updated":"2025-09-08T08:58:20Z","date_published":"2024-08-14T00:00:00Z","month":"08","article_type":"original","department":[{"_id":"TiBr"}],"article_number":"e12975","article_processing_charge":"Yes (via OA deal)","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","file":[{"date_updated":"2024-08-21T06:36:40Z","creator":"dernst","file_size":438751,"checksum":"90437e19f57520b4d66ca62408f6c81e","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"17454","file_name":"2024_JourLondonMathSoc_Wang.pdf","date_created":"2024-08-21T06:36:40Z","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"corr_author":"1","has_accepted_license":"1","status":"public","year":"2024","issue":"3","isi":1,"scopus_import":"1","date_created":"2024-08-20T08:41:40Z","day":"14","abstract":[{"lang":"eng","text":"Let  F be a diagonal cubic form over Z in six variables. From the dual variety in the delta method of Duke–Friedlander–Iwaniec and Heath‐Brown, we unconditionally extract a weighted count of certain special integral zeros of F in regions of diameter X - 8 . Heath‐Brown did the same in four variables, but our analysis differs and captures some novel features. We also put forth an axiomatic framework for more general F."}],"volume":110,"file_date_updated":"2024-08-21T06:36:40Z","language":[{"iso":"eng"}],"title":"Special cubic zeros and the dual variety","intvolume":"       110","arxiv":1,"external_id":{"isi":["001310529600001"],"arxiv":["2108.03396"]},"ddc":["512"],"acknowledgement":"This paper is an important component of the thesis work described in [25]; many of my acknowledgements there apply here as well. I also thank my advisor, Peter Sarnak, for many helpful suggestions and questions on the exposition, references, assumptions, and scope of (various drafts of) the present work. I am also grateful to Trevor Wooley for providing some helpful general comments on special subvarieties and the reference [24]. I thank Tim Browning for inspiring part of the current title of the paper. Finally, thanks are due to the referee for providing many helpful suggestions. This work was partially supported by NSF grant DMS-1802211, and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant AgreementNo. 101034413.","citation":{"chicago":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” <i>Journal of the London Mathematical Society</i>. Wiley, 2024. <a href=\"https://doi.org/10.1112/jlms.12975\">https://doi.org/10.1112/jlms.12975</a>.","short":"V. Wang, Journal of the London Mathematical Society 110 (2024).","ista":"Wang V. 2024. Special cubic zeros and the dual variety. Journal of the London Mathematical Society. 110(3), e12975.","apa":"Wang, V. (2024). Special cubic zeros and the dual variety. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12975\">https://doi.org/10.1112/jlms.12975</a>","ama":"Wang V. Special cubic zeros and the dual variety. <i>Journal of the London Mathematical Society</i>. 2024;110(3). doi:<a href=\"https://doi.org/10.1112/jlms.12975\">10.1112/jlms.12975</a>","mla":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 3, e12975, Wiley, 2024, doi:<a href=\"https://doi.org/10.1112/jlms.12975\">10.1112/jlms.12975</a>.","ieee":"V. Wang, “Special cubic zeros and the dual variety,” <i>Journal of the London Mathematical Society</i>, vol. 110, no. 3. Wiley, 2024."},"type":"journal_article","publication":"Journal of the London Mathematical Society","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"_id":"17447","doi":"10.1112/jlms.12975","author":[{"orcid":"0000-0002-0704-7026","last_name":"Wang","full_name":"Wang, Victor","first_name":"Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9"}],"quality_controlled":"1"},{"publication_identifier":{"issn":["1937-0652"],"eissn":["1944-7833"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1401725,"checksum":"1e3467a14de754bf8d3bff03a015e1ce","creator":"dernst","success":1,"date_updated":"2024-08-21T06:46:56Z","date_created":"2024-08-21T06:46:56Z","file_name":"2024_AlgebraNumberTheory_Pandey.pdf","relation":"main_file","file_id":"17455"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"year":"2024","issue":"2","status":"public","has_accepted_license":"1","date_published":"2024-02-06T00:00:00Z","article_type":"original","month":"02","publication_status":"published","date_updated":"2024-08-21T06:58:43Z","publisher":"Mathematical Sciences Publishers","oa":1,"article_processing_charge":"Yes (via OA deal)","type":"journal_article","publication":"Algebra & Number Theory","citation":{"chicago":"Pandey, Mayank, Victor Wang, and Max Wenqiang Xu. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” <i>Algebra &#38; Number Theory</i>. Mathematical Sciences Publishers, 2024. <a href=\"https://doi.org/10.2140/ant.2024.18.389\">https://doi.org/10.2140/ant.2024.18.389</a>.","short":"M. Pandey, V. Wang, M.W. Xu, Algebra &#38; Number Theory 18 (2024) 389–408.","ista":"Pandey M, Wang V, Xu MW. 2024. Partial sums of typical multiplicative functions over short moving intervals. Algebra &#38; Number Theory. 18(2), 389–408.","apa":"Pandey, M., Wang, V., &#38; Xu, M. W. (2024). Partial sums of typical multiplicative functions over short moving intervals. <i>Algebra &#38; Number Theory</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/ant.2024.18.389\">https://doi.org/10.2140/ant.2024.18.389</a>","ama":"Pandey M, Wang V, Xu MW. Partial sums of typical multiplicative functions over short moving intervals. <i>Algebra &#38; Number Theory</i>. 2024;18(2):389-408. doi:<a href=\"https://doi.org/10.2140/ant.2024.18.389\">10.2140/ant.2024.18.389</a>","mla":"Pandey, Mayank, et al. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” <i>Algebra &#38; Number Theory</i>, vol. 18, no. 2, Mathematical Sciences Publishers, 2024, pp. 389–408, doi:<a href=\"https://doi.org/10.2140/ant.2024.18.389\">10.2140/ant.2024.18.389</a>.","ieee":"M. Pandey, V. Wang, and M. W. Xu, “Partial sums of typical multiplicative functions over short moving intervals,” <i>Algebra &#38; Number Theory</i>, vol. 18, no. 2. Mathematical Sciences Publishers, pp. 389–408, 2024."},"acknowledgement":"We thank Andrew Granville and the anonymous referee for many detailed comments that led us to significantly improve the results and presentation of our work. We thank and Adam Harper for helpful discussions and useful comments and corrections on earlier versions. We also thank Yuqiu Fu, Larry Guth, Kannan Soundararajan, Katharine Woo, and Liyang Yang for helpful discussions. Finally, we thank Peter Sarnak for introducing us (the authors) to each other during the “50 Years of Number Theory and Random Matrix Theory” Conference at IAS and making the collaboration possible. \r\nOpen Access made possible by participating institutions via Subscribe to Open.","ddc":["510"],"external_id":{"arxiv":["2207.11758"]},"arxiv":1,"intvolume":"        18","quality_controlled":"1","author":[{"full_name":"Pandey, Mayank","first_name":"Mayank","last_name":"Pandey"},{"last_name":"Wang","orcid":"0000-0002-0704-7026","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","first_name":"Victor","full_name":"Wang, Victor"},{"full_name":"Xu, Max Wenqiang","first_name":"Max Wenqiang","last_name":"Xu"}],"page":"389-408","doi":"10.2140/ant.2024.18.389","_id":"17449","extern":"1","scopus_import":"1","title":"Partial sums of typical multiplicative functions over short moving intervals","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.11758"}],"language":[{"iso":"eng"}],"file_date_updated":"2024-08-21T06:46:56Z","volume":18,"day":"06","abstract":[{"text":"We prove that the $k$-th positive integer moment of partial sums of Steinhaus random multiplicative functions over the interval $(x, x+H]$ matches the corresponding Gaussian moment, as long as $H\\ll x/(\\log x)^{2k^2+2+o(1)}$ and $H$ tends to infinity with $x$. We show that properly normalized partial sums of typical multiplicative functions arising from realizations of random multiplicative functions have Gaussian limiting distribution in short moving intervals $(x, x+H]$ with $H\\ll X/(\\log X)^{W(X)}$ tending to infinity with $X$, where $x$ is uniformly chosen from $\\{1,2,\\dots, X\\}$, and $W(X)$ tends to infinity with $X$ arbitrarily slowly. This makes some initial progress on a recent question of Harper.","lang":"eng"}],"date_created":"2024-08-20T08:48:26Z"},{"_id":"17456","quality_controlled":"1","author":[{"full_name":"Markov, Ilia","first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","last_name":"Markov"},{"last_name":"Alimohammadi","first_name":"Kaveh","full_name":"Alimohammadi, Kaveh"},{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias","first_name":"Elias","last_name":"Frantar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"citation":{"chicago":"Markov, Ilia, Kaveh Alimohammadi, Elias Frantar, and Dan-Adrian Alistarh. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” In <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6. Association for Computing Machinery, 2024.","short":"I. Markov, K. Alimohammadi, E. Frantar, D.-A. Alistarh, in:, P. Gibbons, G. Pekhimenko, C. De Sa (Eds.), Proceedings of Machine Learning and Systems , Association for Computing Machinery, 2024.","ista":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. 2024. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. Proceedings of Machine Learning and Systems . MLSys: Machine Learning and Systems vol. 6.","apa":"Markov, I., Alimohammadi, K., Frantar, E., &#38; Alistarh, D.-A. (2024). L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In P. Gibbons, G. Pekhimenko, &#38; C. De Sa (Eds.), <i>Proceedings of Machine Learning and Systems </i> (Vol. 6). Athens, Greece: Association for Computing Machinery.","ama":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In: Gibbons P, Pekhimenko G, De Sa C, eds. <i>Proceedings of Machine Learning and Systems </i>. Vol 6. Association for Computing Machinery; 2024.","ieee":"I. Markov, K. Alimohammadi, E. Frantar, and D.-A. Alistarh, “L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning,” in <i>Proceedings of Machine Learning and Systems </i>, Athens, Greece, 2024, vol. 6.","mla":"Markov, Ilia, et al. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons et al., vol. 6, Association for Computing Machinery, 2024."},"ddc":["000"],"external_id":{"arxiv":["2210.17357"]},"arxiv":1,"intvolume":"         6","type":"conference","publication":"Proceedings of Machine Learning and Systems ","day":"01","abstract":[{"text":"Data-parallel distributed training of deep neural networks (DNN) has gained very widespread adoption, but can still experience communication bottlenecks. To address this issue, entire families of compression mechanisms have been developed, including quantization, sparsification, and low-rank approximation, some of which are seeing significant practical adoption. Despite this progress, almost all known compression schemes apply compression uniformly across DNN layers, although layers are heterogeneous in terms of parameter count and their impact on model accuracy.In this work, we provide a general framework for adapting the degree of compression across the model's layers dynamically during training, improving the overall compression, while leading to substantial speedups, without sacrificing accuracy. Our framework, called L-GreCo, is based on an adaptive algorithm, which automatically picks the optimal compression parameters for model layers guaranteeing the best compression ratio while satisfying an error constraint. Extensive experiments over image classification and language modeling tasks shows that L-GreCo is effective across all existing families of compression methods, and achieves up to 2.5\r\n×\r\n training speedup and up to 5\r\n×\r\n compression improvement over efficient implementations of existing approaches, while recovering full accuracy. Moreover, L-GreCo is complementary to existing adaptive algorithms, improving their compression ratio by 50\\% and practical throughput by 66\\%. An anonymized implementation is available at https://github.com/LGrCo/L-GreCo.","lang":"eng"}],"date_created":"2024-08-22T08:29:25Z","title":"L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning","main_file_link":[{"open_access":"1","url":"https://proceedings.mlsys.org/paper_files/paper/2024/hash/9069a8976ff06f6443e7f4172990a580-Abstract-Conference.html"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17490"}]},"language":[{"iso":"eng"}],"volume":6,"editor":[{"full_name":"Gibbons, P.","first_name":"P.","last_name":"Gibbons"},{"full_name":"Pekhimenko, G.","first_name":"G.","last_name":"Pekhimenko"},{"first_name":"C.","full_name":"De Sa, C.","last_name":"De Sa"}],"corr_author":"1","year":"2024","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","conference":{"name":"MLSys: Machine Learning and Systems","start_date":"2024-04-22","location":"Athens, Greece","end_date":"2024-04-22"},"department":[{"_id":"DaAl"}],"oa":1,"publisher":"Association for Computing Machinery","month":"04","date_published":"2024-04-01T00:00:00Z","publication_status":"published","date_updated":"2026-06-18T17:55:24Z"},{"publisher":"Wolters Kluwer","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"date_published":"2024-09-01T00:00:00Z","month":"09","article_type":"original","date_updated":"2025-09-08T08:59:37Z","publication_status":"published","department":[{"_id":"RySh"}],"article_processing_charge":"Yes","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"gold","file":[{"date_created":"2025-01-09T13:42:42Z","file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","relation":"main_file","file_id":"18815","file_size":855818,"checksum":"1e6d1230e0387f72752e3268f5330c9e","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"date_updated":"2025-01-09T13:42:42Z"}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","publication_identifier":{"eissn":["2332-7812"]},"has_accepted_license":"1","issue":"5","status":"public","year":"2024","pmid":1,"isi":1,"scopus_import":"1","abstract":[{"text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening.","lang":"eng"}],"day":"01","date_created":"2024-08-25T22:01:07Z","file_date_updated":"2025-01-09T13:42:42Z","volume":11,"title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","DOAJ_listed":"1","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2023.10.04.560631"}]},"language":[{"iso":"eng"}],"intvolume":"        11","citation":{"ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology and Neuroinflammation</i>. 2024;11(5):e200284. doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology and Neuroinflammation</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>","ieee":"A. Ritzau-Jost <i>et al.</i>, “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” <i>Neurology, Neuroimmunology and Neuroinflammation</i>, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology and Neuroinflammation</i>, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>.","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology and Neuroinflammation 11 (2024) e200284.","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology and Neuroinflammation</i>. Wolters Kluwer, 2024. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>.","ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. 11(5), e200284."},"acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","ddc":["570"],"external_id":{"isi":["001291908600001"],"pmid":["39141878"]},"type":"journal_article","publication":"Neurology, Neuroimmunology and Neuroinflammation","project":[{"_id":"05970B30-7A3F-11EA-A408-12923DDC885E","name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638"}],"doi":"10.1212/NXI.0000000000200284","_id":"17457","page":"e200284","author":[{"full_name":"Ritzau-Jost, Andreas","first_name":"Andreas","last_name":"Ritzau-Jost"},{"full_name":"Gsell, Felix","first_name":"Felix","last_name":"Gsell"},{"last_name":"Sell","full_name":"Sell, Josefine","first_name":"Josefine"},{"last_name":"Sachs","first_name":"Stefan","full_name":"Sachs, Stefan"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"full_name":"Kirmann, Toni","first_name":"Toni","last_name":"Kirmann"},{"last_name":"Maaß","first_name":"Sebastian","full_name":"Maaß, Sebastian"},{"first_name":"Sarosh R.","full_name":"Irani, Sarosh R.","last_name":"Irani"},{"last_name":"Werner","full_name":"Werner, Christian","first_name":"Christian"},{"last_name":"Geis","full_name":"Geis, Christian","first_name":"Christian"},{"last_name":"Sauer","full_name":"Sauer, Markus","first_name":"Markus"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"last_name":"Hallermann","first_name":"Stefan","full_name":"Hallermann, Stefan"}],"quality_controlled":"1"},{"oa":1,"department":[{"_id":"BeVi"}],"article_number":"dev202891","article_processing_charge":"Yes (in subscription journal)","month":"08","date_published":"2024-08-14T00:00:00Z","article_type":"original","date_updated":"2025-09-08T08:58:58Z","publication_status":"published","publisher":"The Company of Biologists","status":"public","issue":"15","year":"2024","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"file":[{"date_created":"2024-08-28T10:32:16Z","file_name":"2024_Development_Cecalev.pdf","relation":"main_file","file_id":"17464","checksum":"5e428bda0440d3f957c694b315a8f2a9","file_size":2085135,"access_level":"open_access","content_type":"application/pdf","creator":"cchlebak","success":1,"date_updated":"2024-08-28T10:32:16Z"}],"oa_version":"Published Version","file_date_updated":"2024-08-28T10:32:16Z","volume":151,"title":"Compensation of gene dosage on the mammalian X","language":[{"iso":"eng"}],"day":"14","abstract":[{"text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.","lang":"eng"}],"date_created":"2024-08-25T22:01:07Z","isi":1,"scopus_import":"1","pmid":1,"author":[{"last_name":"Cecalev","full_name":"Cecalev, Daniela","first_name":"Daniela"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"last_name":"Galupa","full_name":"Galupa, Rafael","first_name":"Rafael"}],"quality_controlled":"1","doi":"10.1242/dev.202891","_id":"17458","type":"journal_article","publication":"Development","intvolume":"       151","citation":{"ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>.","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. The Company of Biologists, 2024.","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>"},"acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","ddc":["599"],"external_id":{"isi":["001292608800003"],"pmid":["39140247"]}},{"page":"1670-1678","author":[{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"last_name":"Whitley","full_name":"Whitley, Kevin D.","first_name":"Kevin D."},{"orcid":"0000-0001-9198-2182 ","last_name":"Radler","full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Holden","full_name":"Holden, Séamus","first_name":"Séamus"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"quality_controlled":"1","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"_id":"17460","doi":"10.1038/s41567-024-02597-8","type":"journal_article","publication":"Nature Physics","intvolume":"        20","external_id":{"isi":["001289394500005"],"pmid":["39416851"]},"ddc":["570"],"acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","citation":{"short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>.","ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. 2024;20:1670-1678. doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., &#38; Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>","ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1670–1678, 2024.","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>."},"volume":20,"file_date_updated":"2025-04-14T06:06:35Z","language":[{"iso":"eng"}],"title":"Self-organization of mortal filaments and its role in bacterial division ring formation","date_created":"2024-08-25T22:01:08Z","abstract":[{"lang":"eng","text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments."}],"day":"01","isi":1,"scopus_import":"1","pmid":1,"year":"2024","status":"public","corr_author":"1","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"OA_place":"publisher","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","file":[{"file_name":"2024_NaturePhysics_VanhilleCampos.pdf","date_created":"2025-04-14T06:06:35Z","relation":"main_file","file_id":"19556","creator":"dernst","content_type":"application/pdf","checksum":"c4842152e2b90d67f48ea8c9ed7c473b","access_level":"open_access","file_size":8058249,"success":1,"date_updated":"2025-04-14T06:06:35Z"}],"oa":1,"department":[{"_id":"AnSa"},{"_id":"MaLo"}],"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","APC_amount":"12348 EUR","date_updated":"2025-09-08T09:02:20Z","date_published":"2024-10-01T00:00:00Z","article_type":"original","month":"10","ec_funded":1,"publisher":"Springer Nature"},{"corr_author":"1","has_accepted_license":"1","issue":"9","year":"2024","status":"public","oa_version":"Published Version","file":[{"relation":"main_file","file_name":"2024_TrendsParasitology_Cremer.pdf","date_created":"2025-01-09T13:46:05Z","file_id":"18816","success":1,"creator":"dernst","checksum":"362fc994e5df66caf3025b7dc437b647","content_type":"application/pdf","access_level":"open_access","file_size":1068464,"date_updated":"2025-01-09T13:46:05Z"}],"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["1471-4922"],"eissn":["1471-5007"]},"OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SyCr"}],"oa":1,"publisher":"Elsevier","date_updated":"2025-09-08T09:01:42Z","publication_status":"published","article_type":"original","month":"09","date_published":"2024-09-01T00:00:00Z","_id":"17461","doi":"10.1016/j.pt.2024.07.014","quality_controlled":"1","author":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982"}],"page":"780-787","ddc":["570"],"external_id":{"pmid":["39152078"],"isi":["001307815700001"]},"acknowledgement":"We thank Koos Boomsma and two anonymous reviewers for their constructive comments on the manuscript.","citation":{"short":"S. Cremer, C. Pull, Trends in Parasitology 40 (2024) 780–787.","chicago":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>.","ista":"Cremer S, Pull C. 2024. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 40(9), 780–787.","ama":"Cremer S, Pull C. Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. 2024;40(9):780-787. doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>","apa":"Cremer, S., &#38; Pull, C. (2024). Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>","ieee":"S. Cremer and C. Pull, “Unconditional versus condition-dependent social immunity,” <i>Trends in Parasitology</i>, vol. 40, no. 9. Elsevier, pp. 780–787, 2024.","mla":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>, vol. 40, no. 9, Elsevier, 2024, pp. 780–87, doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>."},"intvolume":"        40","type":"journal_article","publication":"Trends in Parasitology","date_created":"2024-08-25T22:01:08Z","abstract":[{"text":"Socially living animals can counteract disease through cooperative defences, leading to social immunity that collectively exceeds the sum of individual defences. In superorganismal colonies of social insects with permanent caste separation between reproductive queen(s) and nonreproducing workers, workers are obligate altruists and thus engage in unconditional social immunity, including highly specialised and self-sacrificial hygiene behaviours. Contrastingly, cooperation is facultative in cooperatively breeding families, where all members are reproductively totipotent but offspring transiently forgo reproduction to help their parents rear more siblings. Here, helpers should either express condition-dependent social immunity or disperse to pursue independent reproduction. We advocate inclusive fitness theory as a framework to predict when and how indirect fitness gains may outweigh direct fitness costs, thus favouring conditional social immunity.","lang":"eng"}],"day":"01","language":[{"iso":"eng"}],"title":"Unconditional versus condition-dependent social immunity","volume":40,"file_date_updated":"2025-01-09T13:46:05Z","pmid":1,"scopus_import":"1","isi":1},{"publication_status":"published","date_updated":"2025-09-08T09:01:00Z","date_published":"2024-09-01T00:00:00Z","article_type":"original","month":"09","ec_funded":1,"publisher":"Society for Industrial and Applied Mathematics","oa":1,"department":[{"_id":"JuFi"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1540-3459"],"eissn":["1540-3467"]},"OA_place":"repository","OA_type":"green","oa_version":"Preprint","status":"public","year":"2024","issue":"3","corr_author":"1","isi":1,"scopus_import":"1","volume":22,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2309.06798","open_access":"1"}],"language":[{"iso":"eng"}],"title":"Artificial boundary conditions for random elliptic systems with correlated coefficient field","date_created":"2024-08-25T22:01:08Z","abstract":[{"text":"We are interested in numerical algorithms for computing the electrical field generated by a charge distribution localized on scale l in an infinite heterogeneous correlated random medium, in a situation where the medium is only known in a box of diameter L >>l around the support of the charge. We show that the algorithm in [J. Lu, F. Otto, and L. Wang, Optimal Artificial Boundary Conditions Based on Second-Order Correctors for Three Dimensional Random Ellilptic Media, preprint, arXiv:2109.01616, 2021], suggesting optimal Dirichlet boundary conditions motivated by the multipole expansion [P. Bella, A. Giunti, and F. Otto, Comm. Partial Differential Equations, 45 (2020), pp. 561–640], still performs well in correlated media. With overwhelming probability, we obtain a convergence rate in terms of l, L, and the size of the correlations for which optimality is supported with numerical simulations. These estimates are provided for ensembles which satisfy a multiscale logarithmic Sobolev inequality, where our main tool is an extension of the semigroup estimates in [N. Clozeau, Stoch. Partial Differ. Equ. Anal. Comput., 11 (2023), pp. 1254–1378]. As part of our strategy, we construct sublinear second-order correctors in this correlated setting, which is of independent interest.","lang":"eng"}],"day":"01","type":"journal_article","publication":"Multiscale Modeling and Simulation","intvolume":"        22","arxiv":1,"external_id":{"isi":["001285416500001"],"arxiv":["2309.06798"]},"acknowledgement":"We would like to thank our affiliations, Institute of Science and Technology Austria and Max Planck Institute for Mathematics in the Sciences, for supporting the authors’ visits to each other, which greatly facilitated this work. We would like to thank Marc Josien and Quinn Winters for assistance in numerical implementation.","citation":{"ista":"Clozeau N, Wang L. 2024. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 22(3), 973–1029.","short":"N. Clozeau, L. Wang, Multiscale Modeling and Simulation 22 (2024) 973–1029.","chicago":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” <i>Multiscale Modeling and Simulation</i>. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/23M1603819\">https://doi.org/10.1137/23M1603819</a>.","ieee":"N. Clozeau and L. Wang, “Artificial boundary conditions for random elliptic systems with correlated coefficient field,” <i>Multiscale Modeling and Simulation</i>, vol. 22, no. 3. Society for Industrial and Applied Mathematics, pp. 973–1029, 2024.","mla":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” <i>Multiscale Modeling and Simulation</i>, vol. 22, no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 973–1029, doi:<a href=\"https://doi.org/10.1137/23M1603819\">10.1137/23M1603819</a>.","ama":"Clozeau N, Wang L. Artificial boundary conditions for random elliptic systems with correlated coefficient field. <i>Multiscale Modeling and Simulation</i>. 2024;22(3):973-1029. doi:<a href=\"https://doi.org/10.1137/23M1603819\">10.1137/23M1603819</a>","apa":"Clozeau, N., &#38; Wang, L. (2024). Artificial boundary conditions for random elliptic systems with correlated coefficient field. <i>Multiscale Modeling and Simulation</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/23M1603819\">https://doi.org/10.1137/23M1603819</a>"},"author":[{"full_name":"Clozeau, Nicolas","first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","last_name":"Clozeau"},{"last_name":"Wang","full_name":"Wang, Lihan","first_name":"Lihan"}],"page":"973-1029","quality_controlled":"1","project":[{"grant_number":"948819","call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"_id":"17462","doi":"10.1137/23M1603819"},{"day":"22","abstract":[{"lang":"eng","text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry."}],"date_created":"2024-08-25T22:01:08Z","title":"De novo design of allosterically switchable protein assemblies","language":[{"iso":"eng"}],"file_date_updated":"2024-09-09T12:01:14Z","volume":632,"pmid":1,"scopus_import":"1","isi":1,"doi":"10.1038/s41586-024-07813-2","_id":"17463","quality_controlled":"1","author":[{"last_name":"Pillai","first_name":"Arvind","full_name":"Pillai, Arvind"},{"first_name":"Abbas","full_name":"Idris, Abbas","last_name":"Idris"},{"last_name":"Philomin","full_name":"Philomin, Annika","first_name":"Annika"},{"first_name":"Connor","full_name":"Weidle, Connor","last_name":"Weidle"},{"last_name":"Skotheim","full_name":"Skotheim, Rebecca","first_name":"Rebecca"},{"first_name":"Philip J.Y.","full_name":"Leung, Philip J.Y.","last_name":"Leung"},{"full_name":"Broerman, Adam","first_name":"Adam","last_name":"Broerman"},{"first_name":"Cullen","full_name":"Demakis, Cullen","last_name":"Demakis"},{"full_name":"Borst, Andrew J.","first_name":"Andrew J.","last_name":"Borst"},{"first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"page":"911–920 ","citation":{"ieee":"A. Pillai <i>et al.</i>, “De novo design of allosterically switchable protein assemblies,” <i>Nature</i>, vol. 632. Springer Nature, pp. 911–920, 2024.","mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>, vol. 632, Springer Nature, 2024, pp. 911–920, doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. <i>Nature</i>. 2024;632:911–920. doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>","apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920.","chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>."},"acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","ddc":["570"],"external_id":{"pmid":["39143214"],"isi":["001300534300019"]},"intvolume":"       632","publication":"Nature","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"FlPr"}],"oa":1,"publisher":"Springer Nature","article_type":"original","month":"08","date_published":"2024-08-22T00:00:00Z","publication_status":"published","date_updated":"2025-09-08T09:00:16Z","has_accepted_license":"1","corr_author":"1","year":"2024","status":"public","file":[{"file_id":"18005","date_created":"2024-09-09T12:01:14Z","file_name":"2024_Nature_Pillai.pdf","relation":"main_file","date_updated":"2024-09-09T12:01:14Z","access_level":"open_access","file_size":16572040,"checksum":"39127601621a360ec0edc538627eb211","content_type":"application/pdf","creator":"dernst","success":1}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"citation":{"ama":"Desaules J-YM. Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>","apa":"Desaules, J.-Y. M. (2024). Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>","mla":"Desaules, Jean-Yves Marc. <i>Data for “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>.","ieee":"J.-Y. M. Desaules, “Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.’” Institute of Science and Technology Austria, 2024.","short":"J.-Y.M. Desaules, (2024).","chicago":"Desaules, Jean-Yves Marc. “Data for ‘Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>.","ista":"Desaules J-YM. 2024. Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>."},"file":[{"relation":"main_file","file_name":"FiguresData.zip","date_created":"2024-08-30T12:55:37Z","file_id":"17472","success":1,"creator":"jdesaule","content_type":"application/zip","file_size":322400,"checksum":"2bd49ce5a63f1951c1ed3d89cce4fe27","access_level":"open_access","date_updated":"2024-08-30T12:55:37Z"},{"success":1,"access_level":"open_access","checksum":"c2ba113a241e98c394cc3ca21f3fa126","content_type":"text/plain","file_size":1368,"creator":"jdesaule","date_updated":"2024-08-30T13:19:57Z","relation":"main_file","date_created":"2024-08-30T13:19:57Z","file_name":"readme.txt","file_id":"17473"}],"oa_version":"Published Version","ddc":["530"],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","type":"research_data","doi":"10.15479/AT:ISTA:17471","_id":"17471","has_accepted_license":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"author":[{"first_name":"Jean-Yves Marc","full_name":"Desaules, Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375","last_name":"Desaules"}],"year":"2024","status":"public","publisher":"Institute of Science and Technology Austria","ec_funded":1,"month":"08","date_published":"2024-08-30T00:00:00Z","contributor":[{"first_name":"Ruizhe","contributor_type":"researcher","last_name":"Shen"},{"first_name":"Fang","contributor_type":"researcher","last_name":"Qin"},{"orcid":"0000-0002-3749-6375","last_name":"Desaules","contributor_type":"researcher","first_name":"Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80"},{"first_name":"Zlatko","contributor_type":"researcher","last_name":"Papić"},{"first_name":"Ching Hua","contributor_type":"researcher","last_name":"Lee"}],"date_updated":"2026-06-10T07:52:53Z","abstract":[{"lang":"eng","text":"Mechanisms for suppressing thermalization in disorder-free many-body systems, such as Hilbert space fragmentation and quantum many-body scars, have recently attracted much interest in foundations of quantum statistical physics and potential quantum information processing applications. However,  their sensitivity to realistic effects such as finite temperature remains largely unexplored. Here, we have utilized IBM's Kolkata quantum processor to demonstrate an unexpected robustness of quantum many-body scars at finite temperatures when the system is prepared in a thermal Gibbs ensemble. We identify such robustness in the PXP model, which describes quantum many-body scars in experimental systems of Rydberg atom arrays and ultracold atoms in tilted Bose--Hubbard optical lattices. By contrast, other theoretical models which host exact quantum many-body scars are found to lack such robustness, and their scarring properties quickly decay with temperature. Our study sheds light on the important differences between scarred models in terms of their algebraic structures, which impacts their resilience to finite temperature."}],"article_processing_charge":"No","day":"30","date_created":"2024-08-30T12:59:43Z","department":[{"_id":"MaSe"}],"title":"Data for \"Enhanced many-body quantum scars from the non-Hermitian Fock skin effect\"","related_material":{"record":[{"status":"public","id":"18627","relation":"used_in_publication"}]},"oa":1,"file_date_updated":"2024-08-30T13:19:57Z","keyword":["quantum many-body scars","non-equilibrium physics","non-Hermitian physics"]}]