[{"ddc":["570"],"status":"public","DOAJ_listed":"1","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"year":"2025","author":[{"full_name":"Najjar, Hadil","last_name":"Najjar","first_name":"Hadil"},{"full_name":"Weiß, Sarah","first_name":"Sarah","last_name":"Weiß"},{"first_name":"Ferdinand","last_name":"Horvath","id":"b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e","full_name":"Horvath, Ferdinand"},{"full_name":"Hopl, Valentina","first_name":"Valentina","last_name":"Hopl"},{"first_name":"Adéla","last_name":"Tiffner","full_name":"Tiffner, Adéla"},{"last_name":"Höbarth","first_name":"Lorenz","full_name":"Höbarth, Lorenz"},{"first_name":"Julia","last_name":"Söllner","full_name":"Söllner, Julia"},{"first_name":"Maximilian","last_name":"Fröhlich","full_name":"Fröhlich, Maximilian"},{"full_name":"Prantl, Magdalena","last_name":"Prantl","first_name":"Magdalena"},{"full_name":"Müller, Nora","last_name":"Müller","first_name":"Nora"},{"first_name":"Yuliia","last_name":"Nazarenko","full_name":"Nazarenko, Yuliia"},{"first_name":"Selina","last_name":"Harant","full_name":"Harant, Selina"},{"full_name":"Weissenböck, Lukas","first_name":"Lukas","last_name":"Weissenböck"},{"last_name":"Grabmayr","first_name":"Herwig","full_name":"Grabmayr, Herwig"},{"full_name":"Sallinger, Matthias","last_name":"Sallinger","first_name":"Matthias"},{"first_name":"Lena","last_name":"Maltan","full_name":"Maltan, Lena"},{"first_name":"Linda V.","last_name":"Echefu","full_name":"Echefu, Linda V."},{"first_name":"Tamara","last_name":"Radiskovic","full_name":"Radiskovic, Tamara"},{"last_name":"Leopold","first_name":"Melanie","full_name":"Leopold, Melanie"},{"full_name":"Lindinger, Sonja","last_name":"Lindinger","first_name":"Sonja"},{"full_name":"Humer, Christina","last_name":"Humer","first_name":"Christina"},{"first_name":"Carmen","last_name":"Höglinger","full_name":"Höglinger, Carmen"},{"last_name":"Krobath","first_name":"Heinrich","full_name":"Krobath, Heinrich"},{"full_name":"Renger, Thomas","last_name":"Renger","first_name":"Thomas"},{"first_name":"Isabella","last_name":"Derler","full_name":"Derler, Isabella"}],"volume":6,"publication_identifier":{"eissn":["2666-3864"]},"OA_place":"publisher","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"The Ca2+-release-activated Ca2+ (CRAC) channel Orai1 is activated by interaction with the Ca2+ sensor Stromal Interaction Molecule 1 (STIM1). Owing to the lack of structurally resolved Orai1/STIM1 complexes, the impact of their coupling on individual Orai1 transmembrane domain (TM) movements is unclear. This study investigates STIM1-independent and STIM1-dependent Orai1-TM dynamics using photocrosslinking unnatural amino acids (UAAs) at each individual TM position. We primarily identify CRAC-channel-like currents directly after UAA incorporation or additional UV-light irradiation at TM3 sites that interface with non-pore-lining TMs. Using UAAs combined with conventional site-directed mutagenesis and molecular dynamics simulations, we discover that pore opening involves a widening of interfaces formed by TM3 with non-pore-lining TMs. Orai1 mutants with a UAA in TM3 exhibit weaker STIM1-induced activation after UV exposure, possibly caused by a restricted widening of non-pore-lining TM interfaces. We demonstrate that photocrosslinking UAAs are excellent tools for improving our understanding of key determinants and ion channel dynamics modulating pore opening."}],"acknowledgement":"We thank S. Buchegger for excellent technical assistance. This research was funded by the Austrian Science Fund (FWF) projects https://doi.org/10.55776/P32851, https://doi.org/10.55776/P35900, and https://doi.org/10.55776/P36202 to I.D. and https://doi.org/10.55776/PAT6871323 to A.T. N.M. is funded within the DOC program of the OeAW (Austrian Academy of Science). For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","issue":"6","publisher":"Elsevier","oa":1,"date_created":"2025-06-15T22:01:31Z","file_date_updated":"2025-06-23T10:20:22Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","external_id":{"isi":["001516570500009"]},"day":"18","publication":"Cell Reports Physical Science","citation":{"apa":"Najjar, H., Weiß, S., Horvath, F., Hopl, V., Tiffner, A., Höbarth, L., … Derler, I. (2025). STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>","short":"H. Najjar, S. Weiß, F. Horvath, V. Hopl, A. Tiffner, L. Höbarth, J. Söllner, M. Fröhlich, M. Prantl, N. Müller, Y. Nazarenko, S. Harant, L. Weissenböck, H. Grabmayr, M. Sallinger, L. Maltan, L.V. Echefu, T. Radiskovic, M. Leopold, S. Lindinger, C. Humer, C. Höglinger, H. Krobath, T. Renger, I. Derler, Cell Reports Physical Science 6 (2025).","ieee":"H. Najjar <i>et al.</i>, “STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening,” <i>Cell Reports Physical Science</i>, vol. 6, no. 6. Elsevier, 2025.","chicago":"Najjar, Hadil, Sarah Weiß, Ferdinand Horvath, Valentina Hopl, Adéla Tiffner, Lorenz Höbarth, Julia Söllner, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">https://doi.org/10.1016/j.xcrp.2025.102623</a>.","ama":"Najjar H, Weiß S, Horvath F, et al. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. <i>Cell Reports Physical Science</i>. 2025;6(6). doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>","mla":"Najjar, Hadil, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” <i>Cell Reports Physical Science</i>, vol. 6, no. 6, 102623, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.xcrp.2025.102623\">10.1016/j.xcrp.2025.102623</a>.","ista":"Najjar H, Weiß S, Horvath F, Hopl V, Tiffner A, Höbarth L, Söllner J, Fröhlich M, Prantl M, Müller N, Nazarenko Y, Harant S, Weissenböck L, Grabmayr H, Sallinger M, Maltan L, Echefu LV, Radiskovic T, Leopold M, Lindinger S, Humer C, Höglinger C, Krobath H, Renger T, Derler I. 2025. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science. 6(6), 102623."},"file":[{"file_size":9771117,"date_created":"2025-06-23T10:20:22Z","access_level":"open_access","file_name":"2025_CellReportsPhysicalScience_Najjar.pdf","creator":"dernst","success":1,"checksum":"37ff7c396f966d0ec363e4691d63d402","relation":"main_file","file_id":"19868","date_updated":"2025-06-23T10:20:22Z","content_type":"application/pdf"}],"isi":1,"oa_version":"Published Version","scopus_import":"1","title":"STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening","type":"journal_article","quality_controlled":"1","month":"06","intvolume":"         6","publication_status":"published","date_updated":"2025-09-30T12:53:15Z","_id":"19846","date_published":"2025-06-18T00:00:00Z","article_processing_charge":"Yes","OA_type":"gold","article_number":"102623","doi":"10.1016/j.xcrp.2025.102623","license":"https://creativecommons.org/licenses/by/4.0/"},{"status":"public","ddc":["540"],"author":[{"id":"452e82c6-803f-11ed-ab7e-ca0439e73a5d","last_name":"Palacios Corella","first_name":"Mario","full_name":"Palacios Corella, Mario"},{"id":"a623795e-21fb-11ed-b8a1-a0f51308eed7","last_name":"Echevarría","first_name":"Igor","full_name":"Echevarría, Igor"},{"first_name":"Carla","last_name":"Santana Santos","full_name":"Santana Santos, Carla"},{"full_name":"Schuhmann, Wolfgang","last_name":"Schuhmann","first_name":"Wolfgang"},{"full_name":"Ventosa, Edgar","last_name":"Ventosa","first_name":"Edgar"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"}],"year":"2025","language":[{"iso":"eng"}],"PlanS_conform":"1","corr_author":"1","department":[{"_id":"MaIb"}],"abstract":[{"lang":"eng","text":"Prussian blue (PB) and Prussian blue analogues (PBAs) are a class of porous materials composed of transition metal cations, cyanide ligands, and alkali metal cations. Their ability to intercalate and deintercalate ions within their framework pores, coupled with the adaptability of their crystal structure to electrochemical changes, underpins their success in battery applications. PBAs with Fe or Co as the active site exhibit high redox potentials (vs SHE) and have been extensively explored as cathode materials, with well-documented chemistry, crystal structures, and electrochemical properties. In contrast, PBAs with Cr or Mn as the active site display lower redox potentials and remain significantly underexplored as anode materials. This gap has led to fewer reported compounds and a less comprehensive understanding of their structural and electrochemical behavior, leaving the field relatively opaque. In this perspective, we comprehensively analyze the challenges involved in producing and employing PBAs with low redox potentials as active battery materials. Conversely, we propose numerous horizons and ask fundamental questions that should pave the way for future research to advance the field."}],"issue":"12","acknowledgement":"All the authors acknowledge financial support by the MeBattery project. MeBattery has received funding from the European Innovation Council of the European Union under Grant Agreement No. 101046742. We acknowledge the valuable scientific discussions with Christine Fiedler. M.P.-C. acknowledges that the project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434) with code LCF/BQ/PI24/12040015. E.V. also acknowledges financial support by the Spanish Ministry of Science and Innovation and NextGenerationEU (TED2021-131651B-C21) and Ramón y Cajal award (Ministry of Science and Innovation and European Social Funds, RYC2018-026086-I).","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"volume":37,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","OA_place":"publisher","project":[{"grant_number":"101046742","_id":"eb9fa02e-77a9-11ec-83b8-ab1143e5a30f","name":"MEDIATED BIPHASIC BATTERY"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2025-06-15T22:01:31Z","publisher":"American Chemical Society","oa":1,"file_date_updated":"2025-12-30T08:40:55Z","citation":{"apa":"Palacios Corella, M., Echevarría, I., Santana Santos, C., Schuhmann, W., Ventosa, E., &#38; Ibáñez, M. (2025). Prussian blue analogues as anode materials for battery applications: Complexities and horizons. <i>Chemistry of Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemmater.5c00213\">https://doi.org/10.1021/acs.chemmater.5c00213</a>","short":"M. Palacios Corella, I. Echevarría, C. Santana Santos, W. Schuhmann, E. Ventosa, M. Ibáñez, Chemistry of Materials 37 (2025) 4203–4226.","ieee":"M. Palacios Corella, I. Echevarría, C. Santana Santos, W. Schuhmann, E. Ventosa, and M. Ibáñez, “Prussian blue analogues as anode materials for battery applications: Complexities and horizons,” <i>Chemistry of Materials</i>, vol. 37, no. 12. American Chemical Society, pp. 4203–4226, 2025.","chicago":"Palacios Corella, Mario, Igor Echevarría, Carla Santana Santos, Wolfgang Schuhmann, Edgar Ventosa, and Maria Ibáñez. “Prussian Blue Analogues as Anode Materials for Battery Applications: Complexities and Horizons.” <i>Chemistry of Materials</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.chemmater.5c00213\">https://doi.org/10.1021/acs.chemmater.5c00213</a>.","ama":"Palacios Corella M, Echevarría I, Santana Santos C, Schuhmann W, Ventosa E, Ibáñez M. Prussian blue analogues as anode materials for battery applications: Complexities and horizons. <i>Chemistry of Materials</i>. 2025;37(12):4203-4226. doi:<a href=\"https://doi.org/10.1021/acs.chemmater.5c00213\">10.1021/acs.chemmater.5c00213</a>","mla":"Palacios Corella, Mario, et al. “Prussian Blue Analogues as Anode Materials for Battery Applications: Complexities and Horizons.” <i>Chemistry of Materials</i>, vol. 37, no. 12, American Chemical Society, 2025, pp. 4203–26, doi:<a href=\"https://doi.org/10.1021/acs.chemmater.5c00213\">10.1021/acs.chemmater.5c00213</a>.","ista":"Palacios Corella M, Echevarría I, Santana Santos C, Schuhmann W, Ventosa E, Ibáñez M. 2025. Prussian blue analogues as anode materials for battery applications: Complexities and horizons. Chemistry of Materials. 37(12), 4203–4226."},"isi":1,"file":[{"access_level":"open_access","file_name":"2025_ChemistryMaterials_PalaciosCorella.pdf","date_created":"2025-12-30T08:40:55Z","file_size":8760757,"relation":"main_file","checksum":"902c52a2f52a028436e0acd8a5a4beac","file_id":"20897","creator":"dernst","success":1,"date_updated":"2025-12-30T08:40:55Z","content_type":"application/pdf"}],"external_id":{"isi":["001501830600001"]},"day":"03","publication":"Chemistry of Materials","scopus_import":"1","title":"Prussian blue analogues as anode materials for battery applications: Complexities and horizons","type":"journal_article","page":"4203-4226","oa_version":"Published Version","date_published":"2025-06-03T00:00:00Z","intvolume":"        37","month":"06","quality_controlled":"1","_id":"19847","date_updated":"2025-12-30T08:41:57Z","publication_status":"published","doi":"10.1021/acs.chemmater.5c00213","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid"},{"doi":"10.1007/s10506-025-09458-6","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","date_published":"2025-05-26T00:00:00Z","_id":"19848","date_updated":"2025-09-30T12:52:15Z","publication_status":"epub_ahead","month":"05","quality_controlled":"1","title":"Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification","type":"journal_article","scopus_import":"1","oa_version":"Published Version","isi":1,"citation":{"short":"R. Tinarrage, H. Ennes, L. Resck, L.T. Gomes, J.R. Ponciano, J. Poco, Artificial Intelligence and Law (2025).","apa":"Tinarrage, R., Ennes, H., Resck, L., Gomes, L. T., Ponciano, J. R., &#38; Poco, J. (2025). Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification. <i>Artificial Intelligence and Law</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10506-025-09458-6\">https://doi.org/10.1007/s10506-025-09458-6</a>","ieee":"R. Tinarrage, H. Ennes, L. Resck, L. T. Gomes, J. R. Ponciano, and J. Poco, “Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification,” <i>Artificial Intelligence and Law</i>. Springer Nature, 2025.","chicago":"Tinarrage, Raphaël, Henrique Ennes, Lucas Resck, Lucas T. Gomes, Jean R. Ponciano, and Jorge Poco. “Empirical Analysis of Binding Precedent Efficiency in Brazilian Supreme Court via Case Classification.” <i>Artificial Intelligence and Law</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s10506-025-09458-6\">https://doi.org/10.1007/s10506-025-09458-6</a>.","mla":"Tinarrage, Raphaël, et al. “Empirical Analysis of Binding Precedent Efficiency in Brazilian Supreme Court via Case Classification.” <i>Artificial Intelligence and Law</i>, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s10506-025-09458-6\">10.1007/s10506-025-09458-6</a>.","ama":"Tinarrage R, Ennes H, Resck L, Gomes LT, Ponciano JR, Poco J. Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification. <i>Artificial Intelligence and Law</i>. 2025. doi:<a href=\"https://doi.org/10.1007/s10506-025-09458-6\">10.1007/s10506-025-09458-6</a>","ista":"Tinarrage R, Ennes H, Resck L, Gomes LT, Ponciano JR, Poco J. 2025. Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification. Artificial Intelligence and Law."},"day":"26","publication":"Artificial Intelligence and Law","external_id":{"isi":["001494836700001"],"arxiv":["2407.07004"]},"date_created":"2025-06-15T22:01:31Z","publisher":"Springer Nature","oa":1,"arxiv":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10506-025-09458-6"}],"abstract":[{"text":"Binding precedents (súmulas vinculantes) constitute a juridical instrument unique to the Brazilian legal system and whose objectives include the protection of the Federal Supreme Court against repetitive demands. Studies of the effectiveness of these instruments in decreasing the Court’s exposure to similar cases, however, indicate that they tend to fail in such a direction, with some of the binding precedents seemingly creating new demands. We empirically assess the legal impact of five binding precedents, 11, 14, 17, 26, and 37, at the highest Court level through their effects on the legal subjects they address. This analysis is only possible through the comparison of the Court’s ruling about the precedents’ themes before they are created, which means that these decisions should be detected through techniques of Similar Case Retrieval, which we tackle from the angle of Case Classification. The contributions of this article are therefore twofold: on the mathematical side, we compare the use of different methods of Natural Language Processing — TF-IDF, LSTM, Longformer, and regex — for Case Classification, whereas on the legal side, we contrast the inefficiency of these binding precedents with a set of hypotheses that may justify their repeated usage. We observe that the TF-IDF models performed slightly better than LSTM and Longformer when compared through common metrics; however, the deep learning models were able to detect certain important legal events that TF-IDF missed. On the legal side, we argue that the reasons for binding precedents to fail in responding to repetitive demand are heterogeneous and case-dependent, making it impossible to single out a specific cause. We identify five main hypotheses, which are found in different combinations in each of the precedents studied.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","article_type":"original","publication_identifier":{"issn":["0924-8463"],"eissn":["1572-8382"]},"author":[{"full_name":"Tinarrage, Raphaël","orcid":"0000-0002-1404-1095","first_name":"Raphaël","last_name":"Tinarrage","id":"40ebcc9d-905f-11ef-bf0a-dc475da8a04e"},{"first_name":"Henrique","last_name":"Ennes","full_name":"Ennes, Henrique"},{"full_name":"Resck, Lucas","first_name":"Lucas","last_name":"Resck"},{"full_name":"Gomes, Lucas T.","last_name":"Gomes","first_name":"Lucas T."},{"last_name":"Ponciano","first_name":"Jean R.","full_name":"Ponciano, Jean R."},{"full_name":"Poco, Jorge","first_name":"Jorge","last_name":"Poco"}],"year":"2025","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"corr_author":"1","status":"public"},{"external_id":{"isi":["001514328000004"],"arxiv":["2412.04084"]},"publication":"Physical Review B","day":"18","citation":{"mla":"Babkin, Serafim, et al. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” <i>Physical Review B</i>, vol. 111, no. 21, 214518, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/k4jh-pnxy\">10.1103/k4jh-pnxy</a>.","ama":"Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. Superconducting proximity effect in two-dimensional hole gases. <i>Physical Review B</i>. 2025;111(21). doi:<a href=\"https://doi.org/10.1103/k4jh-pnxy\">10.1103/k4jh-pnxy</a>","chicago":"Babkin, Serafim, Benjamin Joecker, Karsten Flensberg, Maksym Serbyn, and Jeroen Danon. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” <i>Physical Review B</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/k4jh-pnxy\">https://doi.org/10.1103/k4jh-pnxy</a>.","ista":"Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. 2025. Superconducting proximity effect in two-dimensional hole gases. Physical Review B. 111(21), 214518.","ieee":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, and J. Danon, “Superconducting proximity effect in two-dimensional hole gases,” <i>Physical Review B</i>, vol. 111, no. 21. American Physical Society, 2025.","apa":"Babkin, S., Joecker, B., Flensberg, K., Serbyn, M., &#38; Danon, J. (2025). Superconducting proximity effect in two-dimensional hole gases. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/k4jh-pnxy\">https://doi.org/10.1103/k4jh-pnxy</a>","short":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, J. Danon, Physical Review B 111 (2025)."},"isi":1,"file":[{"file_size":1719489,"file_name":"2025_PhysReviewB_Babkin.pdf","access_level":"open_access","date_created":"2025-06-23T10:31:11Z","creator":"dernst","success":1,"file_id":"19869","checksum":"fa8757f4780cfaeb51579c626284a8c1","relation":"main_file","date_updated":"2025-06-23T10:31:11Z","content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","type":"journal_article","title":"Superconducting proximity effect in two-dimensional hole gases","month":"06","intvolume":"       111","quality_controlled":"1","_id":"19852","date_updated":"2025-09-30T12:53:47Z","publication_status":"published","date_published":"2025-06-18T00:00:00Z","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","doi":"10.1103/k4jh-pnxy","article_number":"214518","ddc":["530"],"status":"public","corr_author":"1","department":[{"_id":"MaSe"},{"_id":"GradSch"}],"author":[{"id":"e63d75c3-72ef-11ef-b75a-e303e149911f","last_name":"Babkin","first_name":"Serafim","full_name":"Babkin, Serafim"},{"full_name":"Joecker, Benjamin","last_name":"Joecker","first_name":"Benjamin"},{"full_name":"Flensberg, Karsten","last_name":"Flensberg","first_name":"Karsten"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"}],"language":[{"iso":"eng"}],"year":"2025","volume":111,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","article_type":"original","abstract":[{"lang":"eng","text":"Technology involving hybrid superconductor–semiconductor materials is a promising avenue for engineering quantum devices for information storage, manipulation, and transmission. Proximity-induced superconducting correlations are an essential part of such devices. While the proximity effect in the conduction band of common semiconductors is well understood, its manifestation in confined hole gases, realized for instance in germanium, is an active area of research. Lower-dimensional hole-based systems, particularly in germanium, are emerging as an attractive platform for a variety of solid-state quantum devices, due to their combination of efficient spin and charge control and long coherence times. The recent experimental realization of the proximity effect in germanium thus calls for a theoretical description that is tailored to hole gases. In this work, we propose a simple model to describe proximity-induced superconductivity in two-dimensional hole gases, incorporating both the heavy-hole (HH) and light-hole (LH) bands. We start from the Luttinger–Kohn model, introduce three parameters that characterize hopping across the superconductor–semiconductor interface, and derive explicit intraband and interband effective pairing terms for the HH and LH bands. Unlike previous approaches, our theory provides a quantitative relationship between induced pairings and interface properties. Restricting our general model to an experimentally relevant case where only the HH band crosses the chemical potential, we predict the coexistence of 𝑠-wave and 𝑑-wave singlet pairings, along with triplet-type pairings, and modified Zeeman and Rashba spin–orbit couplings. Our results thus present a starting point for theoretical modeling of quantum devices based on proximitized hole gases, fueling further progress in quantum technology."}],"arxiv":1,"issue":"21","acknowledgement":"We acknowledge useful discussions with Georgios Katsaros, Andrew Higginbotham, and Oliver Schwarze. This research was funded in part by the Austrian Science Fund (FWF) F 86, the European Research Council (Grant Agreement No. 856526), and by the DFG Collaborative Research Center (CRC) 183 Project No. 277101999.","date_created":"2025-06-19T16:54:54Z","publisher":"American Physical Society","oa":1,"file_date_updated":"2025-06-23T10:31:11Z","project":[{"_id":"34a7f947-11ca-11ed-8bc3-c5dc2bbaae25","grant_number":"F8609","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems:  Probing topology in circuits and quantum materials"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1"},{"ec_funded":1,"date_published":"2025-06-12T00:00:00Z","publication_status":"published","date_updated":"2025-09-30T13:36:46Z","_id":"19854","quality_controlled":"1","month":"06","intvolume":"        91","article_number":"11","doi":"10.1007/s00285-025-02235-8","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","file":[{"date_updated":"2025-06-23T11:10:01Z","content_type":"application/pdf","file_name":"2025_JourMathBiology_Pastva.pdf","date_created":"2025-06-23T11:10:01Z","access_level":"open_access","file_size":1243163,"checksum":"a385ef2662f1d0c3497ed3f2721fe594","relation":"main_file","file_id":"19871","creator":"dernst","success":1}],"isi":1,"citation":{"mla":"Pastva, Samuel, et al. “An Open Problem: Why Are Motif-Avoidant Attractors so Rare in Asynchronous Boolean Networks?” <i>Journal of Mathematical Biology</i>, vol. 91, 11, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00285-025-02235-8\">10.1007/s00285-025-02235-8</a>.","ama":"Pastva S, Park KH, Huvar O, Rozum JC, Albert R. An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? <i>Journal of Mathematical Biology</i>. 2025;91. doi:<a href=\"https://doi.org/10.1007/s00285-025-02235-8\">10.1007/s00285-025-02235-8</a>","chicago":"Pastva, Samuel, Kyu Hyong Park, Ondřej Huvar, Jordan C. Rozum, and Réka Albert. “An Open Problem: Why Are Motif-Avoidant Attractors so Rare in Asynchronous Boolean Networks?” <i>Journal of Mathematical Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00285-025-02235-8\">https://doi.org/10.1007/s00285-025-02235-8</a>.","ista":"Pastva S, Park KH, Huvar O, Rozum JC, Albert R. 2025. An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? Journal of Mathematical Biology. 91, 11.","ieee":"S. Pastva, K. H. Park, O. Huvar, J. C. Rozum, and R. Albert, “An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?,” <i>Journal of Mathematical Biology</i>, vol. 91. Springer Nature, 2025.","short":"S. Pastva, K.H. Park, O. Huvar, J.C. Rozum, R. Albert, Journal of Mathematical Biology 91 (2025).","apa":"Pastva, S., Park, K. H., Huvar, O., Rozum, J. C., &#38; Albert, R. (2025). An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? <i>Journal of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00285-025-02235-8\">https://doi.org/10.1007/s00285-025-02235-8</a>"},"publication":"Journal of Mathematical Biology","day":"12","external_id":{"arxiv":["2410.03976"],"isi":["001507009300001"]},"type":"journal_article","title":"An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?","scopus_import":"1","oa_version":"Published Version","acknowledgement":"Ondřej Huvar has been supported by the Czech Science Foundation grant No. GA22-10845S. Samuel Pastva received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. Kyu Hyong Park and Réka Albert have been supported by NSF grant MCB 1715826 and ARO grant 79961-SM-MUR. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the manuscript.","arxiv":1,"abstract":[{"text":"Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular in systems biology due to their ability to model long-term biological phenotypes within a qualitative, predictive framework. Boolean networks model phenotypes as attractors, which are closely linked to minimal trap spaces (inescapable hypercubes in the system’s state space). In biological applications, attractors and minimal trap spaces are typically in one-to-one correspondence. However, this correspondence is not guaranteed: motif-avoidant attractors (MAAs) that lie outside minimal trap spaces are possible. MAAs are rare and poorly understood, despite recent efforts. In this contribution to the BMB & JMB Special Collection “Problems, Progress and Perspectives in Mathematical and Computational Biology”, we summarize the current state of knowledge regarding MAAs and present several novel observations regarding their response to node deletion reductions and linear extensions of edges. We conduct large-scale computational studies on an ensemble of 14 000 models derived from published Boolean models of biological systems, and more than 100 million Random Boolean Networks. Our findings quantify the rarity of MAAs; in particular, we only observed MAAs in biological models after applying standard simplification methods, highlighting the role of network reduction in introducing MAAs into the dynamics. We also show that MAAs are fragile to linear extensions: in sparse networks, even a single linear node can disrupt virtually all MAAs. Motivated by this observation, we improve the upper bound on the number of delays needed to disrupt a motif-avoidant attractor.","lang":"eng"}],"OA_place":"publisher","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0303-6812"],"eissn":["1432-1416"]},"volume":91,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"file_date_updated":"2025-06-23T11:10:01Z","publisher":"Springer Nature","oa":1,"date_created":"2025-06-22T22:02:05Z","status":"public","ddc":["000"],"year":"2025","language":[{"iso":"eng"}],"author":[{"last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"},{"full_name":"Park, Kyu Hyong","last_name":"Park","first_name":"Kyu Hyong"},{"last_name":"Huvar","first_name":"Ondřej","full_name":"Huvar, Ondřej"},{"last_name":"Rozum","first_name":"Jordan C.","full_name":"Rozum, Jordan C."},{"full_name":"Albert, Réka","first_name":"Réka","last_name":"Albert"}],"department":[{"_id":"ToHe"}],"corr_author":"1"},{"publisher":"Oxford University Press","oa":1,"date_created":"2025-06-22T22:02:05Z","file_date_updated":"2025-06-23T11:02:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":540,"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"OA_place":"publisher","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We present indirect constraints on the absolute escape fraction of ionizing photons (f_{\\rm esc}^{\\rm LyC}) of the system GN 42912 which comprises two luminous galaxies (M_{\\rm UV} magnitudes of -20.89 and -20.37) at z\\sim7.5, GN 42912-NE and GN 42912-SW, to determine their contribution to the ionizing photon budget of the Epoch of Reionization (EoR). The high-resolution James Webb Space Telescope NIRSpec and NIRCam observations reveal the two galaxies are separated by only ~0.1\" (0.5 kpc) on the sky and have a 358 km s^{-1} velocity separation. GN 42912-NE and GN 42912-SW are relatively massive for this redshift (log(M_\\ast/M_\\odot) \\sim 8.4 and 8.9, respectively), with gas-phase metallicities of 18 per cent and 23 per cent solar, O_{32} ratios of 5.3 and >5.8, and \\beta slopes of -1.92 and -1.51, respectively. We use the Mg II\\lambda\\lambda2796,2803 doublet to constrain f_{\\rm esc}^{\\rm LyC}. Mg II has an ionization potential close to that of neutral hydrogen and, in the optically thin regime, can be used as an indirect tracer of the LyC leakage. We establish realistic conservative upper limits on f_{\\rm esc}^{\\rm LyC} of 8.5 per cent for GN 42912-NE and 14 per cent for GN 42912-SW. These estimates align with f_{\\rm esc}^{\\rm LyC} trends observed with \\beta, O_{32}, and the H\\beta equivalent width at z<4. The small inferred ionized region sizes (<0.3 pMpc) around both galaxies indicate they have not ionized a significant fraction of the surrounding neutral gas. While these z>7 f_{\\rm esc}^{\\rm LyC} constraints do not decisively determine a specific reionization model, they support a minor contribution from these two relatively luminous galaxies to the EoR."}],"acknowledgement":"This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–03127 for JWST. These observations are associated with program #01871. Support for program #01871 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–03127. SG is grateful for the support enabled by the Harlan J. Smith McDonald fellowship. YI and NG acknowledge support from the Simons Foundation and the National Academy of Sciences of Ukraine (Project 0121U109612). ASL acknowledges support from Knut and Alice Wallenberg Foundation.","arxiv":1,"issue":"3","department":[{"_id":"JoMa"}],"language":[{"iso":"eng"}],"year":"2025","author":[{"last_name":"Gazagnes","first_name":"S.","full_name":"Gazagnes, S."},{"first_name":"J.","last_name":"Chisholm","full_name":"Chisholm, J."},{"full_name":"Endsley, R.","first_name":"R.","last_name":"Endsley"},{"full_name":"Berg, D. A.","last_name":"Berg","first_name":"D. A."},{"full_name":"Leclercq, F.","first_name":"F.","last_name":"Leclercq"},{"last_name":"Jurlin","first_name":"N.","full_name":"Jurlin, N."},{"full_name":"Saldana-Lopez, A.","first_name":"A.","last_name":"Saldana-Lopez"},{"last_name":"Finkelstein","first_name":"S. L.","full_name":"Finkelstein, S. L."},{"full_name":"Flury, S. R.","last_name":"Flury","first_name":"S. R."},{"full_name":"Guseva, N. G.","last_name":"Guseva","first_name":"N. G."},{"full_name":"Henry, A.","last_name":"Henry","first_name":"A."},{"first_name":"Y. I.","last_name":"Izotov","full_name":"Izotov, Y. I."},{"first_name":"I.","last_name":"Jung","full_name":"Jung, I."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"last_name":"Schaerer","first_name":"D.","full_name":"Schaerer, D."}],"ddc":["520"],"status":"public","article_processing_charge":"Yes","OA_type":"gold","doi":"10.1093/mnras/staf768","quality_controlled":"1","intvolume":"       540","month":"07","publication_status":"published","date_updated":"2025-09-30T13:34:20Z","_id":"19855","date_published":"2025-07-01T00:00:00Z","oa_version":"Published Version","scopus_import":"1","page":"2331-2348","type":"journal_article","title":"A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization","external_id":{"arxiv":["2410.03337"],"isi":["001506103600001"]},"publication":"Monthly Notices of the Royal Astronomical Society","day":"01","citation":{"ieee":"S. Gazagnes <i>et al.</i>, “A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 540, no. 3. Oxford University Press, pp. 2331–2348, 2025.","apa":"Gazagnes, S., Chisholm, J., Endsley, R., Berg, D. A., Leclercq, F., Jurlin, N., … Schaerer, D. (2025). A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/staf768\">https://doi.org/10.1093/mnras/staf768</a>","short":"S. Gazagnes, J. Chisholm, R. Endsley, D.A. Berg, F. Leclercq, N. Jurlin, A. Saldana-Lopez, S.L. Finkelstein, S.R. Flury, N.G. Guseva, A. Henry, Y.I. Izotov, I. Jung, J.J. Matthee, D. Schaerer, Monthly Notices of the Royal Astronomical Society 540 (2025) 2331–2348.","ista":"Gazagnes S, Chisholm J, Endsley R, Berg DA, Leclercq F, Jurlin N, Saldana-Lopez A, Finkelstein SL, Flury SR, Guseva NG, Henry A, Izotov YI, Jung I, Matthee JJ, Schaerer D. 2025. A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. Monthly Notices of the Royal Astronomical Society. 540(3), 2331–2348.","mla":"Gazagnes, S., et al. “A Negligible Contribution of Two Luminous z ∼7.5 Galaxies to the Ionizing Photon Budget of Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 540, no. 3, Oxford University Press, 2025, pp. 2331–48, doi:<a href=\"https://doi.org/10.1093/mnras/staf768\">10.1093/mnras/staf768</a>.","ama":"Gazagnes S, Chisholm J, Endsley R, et al. A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization. <i>Monthly Notices of the Royal Astronomical Society</i>. 2025;540(3):2331-2348. doi:<a href=\"https://doi.org/10.1093/mnras/staf768\">10.1093/mnras/staf768</a>","chicago":"Gazagnes, S., J. Chisholm, R. Endsley, D. A. Berg, F. Leclercq, N. Jurlin, A. Saldana-Lopez, et al. “A Negligible Contribution of Two Luminous z ∼7.5 Galaxies to the Ionizing Photon Budget of Reionization.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/mnras/staf768\">https://doi.org/10.1093/mnras/staf768</a>."},"file":[{"success":1,"creator":"dernst","file_id":"19870","relation":"main_file","checksum":"f912c990a0474f1ddf9be6b8a89c7759","file_size":3111567,"access_level":"open_access","file_name":"2025_MonthlyNoticesRAS_Gazagnes.pdf","date_created":"2025-06-23T11:02:59Z","content_type":"application/pdf","date_updated":"2025-06-23T11:02:59Z"}],"isi":1},{"isi":1,"file":[{"content_type":"application/pdf","date_updated":"2025-06-23T11:34:39Z","creator":"dernst","success":1,"checksum":"016f644ed068f8609ded306ad26dbd3f","relation":"main_file","file_id":"19873","file_size":1850797,"access_level":"open_access","date_created":"2025-06-23T11:34:39Z","file_name":"2025_BiologyLetters_Nikolic.pdf"}],"citation":{"apa":"Nikolic, N., Pleska, M., Bergmiller, T., &#38; Guet, C. C. (2025). A bacterial toxin-antitoxin system as a native defence element against RNA phages. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2025.0080\">https://doi.org/10.1098/rsbl.2025.0080</a>","short":"N. Nikolic, M. Pleska, T. Bergmiller, C.C. Guet, Biology Letters 21 (2025).","ieee":"N. Nikolic, M. Pleska, T. Bergmiller, and C. C. Guet, “A bacterial toxin-antitoxin system as a native defence element against RNA phages,” <i>Biology Letters</i>, vol. 21, no. 6. The Royal Society, 2025.","chicago":"Nikolic, Nela, Maros Pleska, Tobias Bergmiller, and Calin C Guet. “A Bacterial Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” <i>Biology Letters</i>. The Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsbl.2025.0080\">https://doi.org/10.1098/rsbl.2025.0080</a>.","ama":"Nikolic N, Pleska M, Bergmiller T, Guet CC. A bacterial toxin-antitoxin system as a native defence element against RNA phages. <i>Biology Letters</i>. 2025;21(6). doi:<a href=\"https://doi.org/10.1098/rsbl.2025.0080\">10.1098/rsbl.2025.0080</a>","mla":"Nikolic, Nela, et al. “A Bacterial Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” <i>Biology Letters</i>, vol. 21, no. 6, 20250080, The Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsbl.2025.0080\">10.1098/rsbl.2025.0080</a>.","ista":"Nikolic N, Pleska M, Bergmiller T, Guet CC. 2025. A bacterial toxin-antitoxin system as a native defence element against RNA phages. Biology Letters. 21(6), 20250080."},"publication":"Biology Letters","day":"11","external_id":{"isi":["001505019800001"],"pmid":["40494395"]},"title":"A bacterial toxin-antitoxin system as a native defence element against RNA phages","type":"journal_article","pmid":1,"scopus_import":"1","oa_version":"Published Version","date_published":"2025-06-11T00:00:00Z","ec_funded":1,"_id":"19857","date_updated":"2025-09-30T13:38:08Z","publication_status":"published","month":"06","intvolume":"        21","quality_controlled":"1","doi":"10.1098/rsbl.2025.0080","article_number":"20250080","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","status":"public","ddc":["570"],"author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"language":[{"iso":"eng"}],"year":"2025","department":[{"_id":"CaGu"}],"corr_author":"1","issue":"6","acknowledged_ssus":[{"_id":"LifeSc"}],"acknowledgement":"This work was supported by ISTFELLOW (People Program – Marie Curie Actions of the European Union’s Seventh Framework Program FP7 under REA grant agreement 291734), the FWF (Austrian Science Fund) Elise Richter Program project number V 738 and the Wellcome Trust Institutional Strategic Support Award (WT105618MA), to N.N. M.P. was a Simons Foundation Fellow of the Life Sciences Research Foundation. We are grateful to Kathrin Tomasek, Lisa Butt, Chris Estell, Alys Jepson, Franklin Nobrega, Stefano Pagliara, Remy Chait, Steve West, Vicki Gold, Josh Eaton, Ivana Gudelj and Rob Beardmore for useful discussions and technical support, as well as to Robin Wright, Christian Fitch and Ben Temperton for sharing equipment. We thank Laurence Van Melderen for sharing the strains. We acknowledge the IST Austria Lab Support Facility, LSI Technical Services Team at the University of Exeter and the Translational Research Exchange @ Exeter (TREE) network. N.N. is grateful to Fabrice Gielen for his support.","abstract":[{"text":"Bacteria have evolved a wide range of defence strategies to protect themselves against bacterial viruses (phages). Most known bacterial antiphage defence systems target phages with DNA genomes, which raises the question of how bacteria defend against phages with RNA genomes. Bacterial toxin–antitoxin systems that cleave intracellular RNA could potentially protect bacteria against RNA phages, but this has not been explored experimentally. In this study, we investigated the role of a model toxin–antitoxin system, MazEF, in protecting Escherichia coli against two RNA phage species. When challenged with these phages, the native presence of mazEF moderately reduced population susceptibility and increased the survival of individual E. coli cells. Genomic analysis further revealed an underrepresentation of the MazF cleavage site in genomes of RNA phages infecting E. coli, indicating selection against cleavage. These results show that, in addition to other physiological roles, RNA-degrading toxin–antitoxin systems may also help defend against RNA phages.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","OA_place":"publisher","publication_identifier":{"issn":["1744-9561"],"eissn":["1744-957X"]},"volume":21,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"V00738","_id":"26956E74-B435-11E9-9278-68D0E5697425","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","call_identifier":"FWF"}],"file_date_updated":"2025-06-23T11:34:39Z","date_created":"2025-06-22T22:02:06Z","oa":1,"publisher":"The Royal Society"},{"isi":1,"file":[{"success":1,"creator":"dernst","file_id":"19872","relation":"main_file","checksum":"ad93a1e052adb29d7bfe8bd551bab193","file_size":995666,"access_level":"open_access","file_name":"2025_LIPIcs_ElHayek.pdf","date_created":"2025-06-23T11:23:29Z","content_type":"application/pdf","date_updated":"2025-06-23T11:23:29Z"}],"citation":{"ista":"El-Hayek A, Hanauer K, Henzinger M. 2025. On b-matching and fully-dynamic maximum k-edge coloring. 4th Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 330, 4.","chicago":"El-Hayek, Antoine, Kathrin Hanauer, and Monika Henzinger. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” In <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">https://doi.org/10.4230/LIPIcs.SAND.2025.4</a>.","ama":"El-Hayek A, Hanauer K, Henzinger M. On b-matching and fully-dynamic maximum k-edge coloring. In: <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">10.4230/LIPIcs.SAND.2025.4</a>","mla":"El-Hayek, Antoine, et al. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 330, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">10.4230/LIPIcs.SAND.2025.4</a>.","short":"A. El-Hayek, K. Hanauer, M. Henzinger, in:, 4th Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025.","apa":"El-Hayek, A., Hanauer, K., &#38; Henzinger, M. (2025). On b-matching and fully-dynamic maximum k-edge coloring. In <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 330). Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2025.4\">https://doi.org/10.4230/LIPIcs.SAND.2025.4</a>","ieee":"A. El-Hayek, K. Hanauer, and M. Henzinger, “On b-matching and fully-dynamic maximum k-edge coloring,” in <i>4th Symposium on Algorithmic Foundations of Dynamic Networks</i>, Liverpool, United Kingdom, 2025, vol. 330."},"day":"02","publication":"4th Symposium on Algorithmic Foundations of Dynamic Networks","external_id":{"arxiv":["2310.01149"],"isi":["001532136900004"]},"title":"On b-matching and fully-dynamic maximum k-edge coloring","type":"conference","scopus_import":"1","oa_version":"Published Version","date_published":"2025-06-02T00:00:00Z","ec_funded":1,"_id":"19858","publication_status":"published","date_updated":"2025-09-30T13:37:28Z","month":"06","intvolume":"       330","quality_controlled":"1","doi":"10.4230/LIPIcs.SAND.2025.4","article_number":"4","article_processing_charge":"No","OA_type":"gold","conference":{"name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","start_date":"2025-06-09","end_date":"2025-06-11","location":"Liverpool, United Kingdom"},"alternative_title":["LIPIcs"],"status":"public","ddc":["000"],"author":[{"first_name":"Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725","last_name":"El-Hayek","full_name":"El-Hayek, Antoine","orcid":"0000-0003-4268-7368"},{"full_name":"Hanauer, Kathrin","first_name":"Kathrin","last_name":"Hanauer"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"}],"language":[{"iso":"eng"}],"year":"2025","department":[{"_id":"MoHe"}],"corr_author":"1","arxiv":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024. This work was further supported by the Federal Ministry of Education and Research (BMBF) project, 6G-RIC: 6G Research and Innovation Cluster, grant 16KISK020K.","abstract":[{"lang":"eng","text":"Given a graph G that undergoes a sequence of edge insertions and deletions, we study the Maximum k-Edge Coloring problem (MkEC): Having access to k different colors, color as many edges of G as possible such that no two adjacent edges share the same color. While this problem is different from simply maintaining a b-matching with b = k, the two problems are related. However, maximum b-matching can be solved efficiently in the static setting, whereas MkEC is NP-hard and even APX-hard for k ≥ 2. \r\nWe present new results on both problems: For b-matching, we show a new integrality gap result and we adapt Wajc’s matching sparsification scheme [David Wajc, 2020] for the case where b is a constant.\r\nUsing these as basis, we give three new algorithms for the dynamic MkEC problem: Our MatchO algorithm builds on the dynamic (2+ε)-approximation algorithm of Bhattacharya, Gupta, and Mohan [Sayan Bhattacharya et al., 2017] for b-matching and achieves a (2+ε)(k+1)/k-approximation in O(poly(log n, ε^-1)) update time against an oblivious adversary. Our MatchA algorithm builds on the dynamic (7+ε)-approximation algorithm by Bhattacharya, Henzinger, and Italiano [Sayan Bhattacharya et al., 2015] for fractional b-matching and achieves a (7+ε)(3k+3)/(3k-1)-approximation in O(poly(log n, ε^-1)) update time against an adaptive adversary. Moreover, our reductions use the dynamic b-matching algorithm as a black box, so any future improvement in the approximation ratio for dynamic b-matching will automatically translate into a better approximation ratio for our algorithms. Finally, we present a greedy algorithm with O(Δ+k) update time, which guarantees a 2.16 approximation factor."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773683"]},"volume":330,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"file_date_updated":"2025-06-23T11:23:29Z","date_created":"2025-06-22T22:02:06Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"oa_version":"Published Version","title":"Color-avoiding percolation on the Erdős–Rényi random graph","type":"journal_article","page":"35-65","scopus_import":"1","publication":"Annales Henri Lebesgue","day":"01","external_id":{"arxiv":["2211.16086 "]},"file":[{"file_name":"2025_AnnalesHenriLebesgue_Lichev.pdf","date_created":"2025-06-23T11:59:22Z","access_level":"open_access","file_size":746588,"file_id":"19875","checksum":"cca22d171b7affa010d17f5e793b0045","relation":"main_file","creator":"dernst","success":1,"date_updated":"2025-06-23T11:59:22Z","content_type":"application/pdf"}],"citation":{"ieee":"L. Lichev and B. Schapira, “Color-avoiding percolation on the Erdős–Rényi random graph,” <i>Annales Henri Lebesgue</i>, vol. 8. École normale supérieure de Rennes, pp. 35–65, 2025.","short":"L. Lichev, B. Schapira, Annales Henri Lebesgue 8 (2025) 35–65.","apa":"Lichev, L., &#38; Schapira, B. (2025). Color-avoiding percolation on the Erdős–Rényi random graph. <i>Annales Henri Lebesgue</i>. École normale supérieure de Rennes. <a href=\"https://doi.org/10.5802/ahl.228\">https://doi.org/10.5802/ahl.228</a>","ista":"Lichev L, Schapira B. 2025. Color-avoiding percolation on the Erdős–Rényi random graph. Annales Henri Lebesgue. 8, 35–65.","mla":"Lichev, Lyuben, and Bruno Schapira. “Color-Avoiding Percolation on the Erdős–Rényi Random Graph.” <i>Annales Henri Lebesgue</i>, vol. 8, École normale supérieure de Rennes, 2025, pp. 35–65, doi:<a href=\"https://doi.org/10.5802/ahl.228\">10.5802/ahl.228</a>.","ama":"Lichev L, Schapira B. Color-avoiding percolation on the Erdős–Rényi random graph. <i>Annales Henri Lebesgue</i>. 2025;8:35-65. doi:<a href=\"https://doi.org/10.5802/ahl.228\">10.5802/ahl.228</a>","chicago":"Lichev, Lyuben, and Bruno Schapira. “Color-Avoiding Percolation on the Erdős–Rényi Random Graph.” <i>Annales Henri Lebesgue</i>. École normale supérieure de Rennes, 2025. <a href=\"https://doi.org/10.5802/ahl.228\">https://doi.org/10.5802/ahl.228</a>."},"OA_type":"gold","article_processing_charge":"Yes","doi":"10.5802/ahl.228","_id":"19859","date_updated":"2025-06-23T12:01:36Z","publication_status":"published","intvolume":"         8","month":"06","quality_controlled":"1","date_published":"2025-06-01T00:00:00Z","department":[{"_id":"MaKw"}],"DOAJ_listed":"1","corr_author":"1","author":[{"id":"9aa8388e-d003-11ee-8458-c4c1d7447977","last_name":"Lichev","first_name":"Lyuben","full_name":"Lichev, Lyuben"},{"first_name":"Bruno","last_name":"Schapira","full_name":"Schapira, Bruno"}],"year":"2025","language":[{"iso":"eng"}],"ddc":["510"],"status":"public","file_date_updated":"2025-06-23T11:59:22Z","date_created":"2025-06-22T22:02:07Z","oa":1,"publisher":"École normale supérieure de Rennes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","OA_place":"publisher","volume":8,"publication_identifier":{"eissn":["2644-9463"]},"arxiv":1,"acknowledgement":"We thank Dieter Mitsche for enlightening discussions, Balázs Ráth for a number of comments\r\nand corrections on a first version of this paper, and an anonymous referee for several useful remarks.","abstract":[{"lang":"eng","text":"We consider a recently introduced model of color-avoiding percolation (abbreviated CA-percolation) defined as follows. Every edge in a graph G is colored in some of k>=2 colors. Two vertices u and v in G are said to be CA-connected if u and v may be connected using any subset of k-1 colors. CA-connectivity defines an equivalence relation on the vertex set of G whose classes are called CA-components.\r\nWe study the component structure of a randomly colored Erdős–Rényi random graph of constant average degree. We distinguish three regimes for the size of the largest component: a supercritical regime, a so-called intermediate regime, and a subcritical regime, in which the largest CA-component has respectively linear, logarithmic, and bounded size. Interestingly, in the subcritical regime, the bound is deterministic and given by the number of colors."}]},{"citation":{"ama":"Surendranadh P, Sachdeva H. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. 2025;79(7):1185-1198. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>","mla":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1185–98, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf047\">10.1093/evolut/qpaf047</a>.","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>.","ista":"Surendranadh P, Sachdeva H. 2025. Effect of assortative mating and sexual selection on polygenic barriers to gene flow. Evolution. 79(7), 1185–1198.","ieee":"P. Surendranadh and H. Sachdeva, “Effect of assortative mating and sexual selection on polygenic barriers to gene flow,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1185–1198, 2025.","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Effect of assortative mating and sexual selection on polygenic barriers to gene flow. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf047\">https://doi.org/10.1093/evolut/qpaf047</a>","short":"P. Surendranadh, H. Sachdeva, Evolution 79 (2025) 1185–1198."},"isi":1,"file":[{"date_updated":"2025-12-30T08:43:33Z","content_type":"application/pdf","date_created":"2025-12-30T08:43:33Z","access_level":"open_access","file_name":"2025_Evolution_Surendranadh.pdf","file_size":2784295,"file_id":"20898","relation":"main_file","checksum":"288ca936cef794d68a55356e70671846","success":1,"creator":"dernst"}],"external_id":{"isi":["001490646300001"]},"publication":"Evolution","day":"01","scopus_import":"1","title":"Effect of assortative mating and sexual selection on polygenic barriers to gene flow","type":"journal_article","page":"1185-1198","oa_version":"Published Version","date_published":"2025-07-01T00:00:00Z","intvolume":"        79","month":"07","quality_controlled":"1","_id":"19876","date_updated":"2025-12-30T08:44:13Z","publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1093/evolut/qpaf047","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","status":"public","ddc":["570"],"author":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X"},{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"}],"year":"2025","language":[{"iso":"eng"}],"corr_author":"1","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Assortative mating and sexual selection are widespread in nature and can play an important role in speciation by facilitating the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified.\r\nHere, we consider a polygenic “magic” trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at\r\nindividual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early-generation hybrids. Our analysis clarifies how “tipping\r\npoints” (characterized by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene\r\nflow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI. "}],"acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"7","acknowledgement":"We thank Nick Barton for useful comments on the manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by Scientific Computing (SciComp).","volume":79,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","status":"public","id":"18712"}]},"article_type":"original","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","date_created":"2025-06-23T13:51:00Z","oa":1,"publisher":"Oxford University Press","file_date_updated":"2025-12-30T08:43:33Z"},{"type":"conference","title":"MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models","page":"239-251","scopus_import":"1","oa_version":"Published Version","isi":1,"file":[{"content_type":"application/pdf","date_updated":"2025-06-24T06:04:17Z","creator":"dernst","success":1,"relation":"main_file","checksum":"a0566ea3c168e8273501a5eb7d767cf8","file_id":"19883","file_size":1330044,"date_created":"2025-06-24T06:04:17Z","file_name":"2025_PPoPP_Frantar.pdf","access_level":"open_access"}],"citation":{"chicago":"Frantar, Elias, Roberto L. Castro, Jiale Chen, Torsten Hoefler, and Dan-Adrian Alistarh. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” In <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, 239–51. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3710848.3710871\">https://doi.org/10.1145/3710848.3710871</a>.","ama":"Frantar E, Castro RL, Chen J, Hoefler T, Alistarh D-A. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. In: <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2025:239-251. doi:<a href=\"https://doi.org/10.1145/3710848.3710871\">10.1145/3710848.3710871</a>","mla":"Frantar, Elias, et al. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2025, pp. 239–51, doi:<a href=\"https://doi.org/10.1145/3710848.3710871\">10.1145/3710848.3710871</a>.","ista":"Frantar E, Castro RL, Chen J, Hoefler T, Alistarh D-A. 2025. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming. PPoPP: Symposium on Principles and Practice of Parallel Programming, 239–251.","short":"E. Frantar, R.L. Castro, J. Chen, T. Hoefler, D.-A. Alistarh, in:, Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2025, pp. 239–251.","apa":"Frantar, E., Castro, R. L., Chen, J., Hoefler, T., &#38; Alistarh, D.-A. (2025). MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. In <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i> (pp. 239–251). Las Vegas, NV, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3710848.3710871\">https://doi.org/10.1145/3710848.3710871</a>","ieee":"E. Frantar, R. L. Castro, J. Chen, T. Hoefler, and D.-A. Alistarh, “MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models,” in <i>Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming</i>, Las Vegas, NV, United States, 2025, pp. 239–251."},"publication":"Proceedings of the 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming","day":"28","external_id":{"arxiv":["2408.11743"],"isi":["001437826500019"]},"doi":"10.1145/3710848.3710871","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","date_published":"2025-02-28T00:00:00Z","_id":"19877","publication_status":"published","date_updated":"2025-09-30T13:41:57Z","month":"02","quality_controlled":"1","author":[{"first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","full_name":"Frantar, Elias"},{"full_name":"Castro, Roberto L.","first_name":"Roberto L.","last_name":"Castro"},{"full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875","first_name":"Jiale","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","last_name":"Chen"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"language":[{"iso":"eng"}],"year":"2025","department":[{"_id":"DaAl"}],"corr_author":"1","status":"public","conference":{"name":"PPoPP: Symposium on Principles and Practice of Parallel Programming","location":"Las Vegas, NV, United States","end_date":"2025-03-05","start_date":"2025-03-01"},"ddc":["000"],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2025-06-24T06:04:17Z","date_created":"2025-06-23T13:51:58Z","publisher":"Association for Computing Machinery","oa":1,"arxiv":1,"acknowledgement":"The authors would like to thank the Neural Magic team, in particular Michael Goin, Alexander Matveev, and Rob Shaw, for support with the vLLM integration. This research was supported in part by generous grants from NVIDIA and Google.","abstract":[{"text":"As inference on Large Language Models (LLMs) emerges as an important workload in machine learning applications, model weight quantization has become a standard technique for efficient GPU deployment. Quantization not only reduces model size, but has also been shown to yield substantial speedups for single-user inference, due to reduced memory movement, with low accuracy impact. Yet, it remains a key open question whether speedups are achievable also in batched settings with multiple parallel clients, which are highly relevant for practical serving. It is unclear whether GPU kernels can be designed to remain practically memory-bound, while supporting the substantially increased compute requirements of batched workloads.\r\nIn this paper, we resolve this question positively by introducing a new design for Mixed-precision Auto-Regressive LINear kernels, called MARLIN. Concretely, given a model whose weights are compressed via quantization to, e.g., 4 bits per element, MARLIN shows that batchsizes up to 16-32 can be practically supported with close to maximum (4×) quantization speedup, and larger batchsizes up to 64-128 with gradually decreasing, but still significant, acceleration. MARLIN accomplishes this via a combination of techniques, such as asynchronous memory access, complex task scheduling and pipelining, and bespoke quantization support. Our experiments show that MARLIN's near-optimal performance on individual LLM layers across different scenarios can also lead to significant end-to-end LLM inference speedups (of up to 2.8×) when integrated with the popular vLLM open-source serving engine. Finally, we show that MARLIN is extensible to further compression techniques, like NVIDIA 2:4 sparsity, leading to additional speedups.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"19884","relation":"software","status":"public"}]},"OA_place":"publisher","publication_identifier":{"isbn":["9798400714436"]}},{"citation":{"chicago":"Melo Velasco, Juan Vicente, Evan Miles, Michael McCarthy, Thomas Shaw, Catriona Louise Fyffe, Adrià Fontrodona-Bach, and Francesca Pellicciotti. “Method Dependence in Thermal Conductivity and Aerodynamic Roughness Length Estimates on a Debris‐covered Glacier.” <i>Journal of Geophysical Research: Earth Surface</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2025jf008360\">https://doi.org/10.1029/2025jf008360</a>.","mla":"Melo Velasco, Juan Vicente, et al. “Method Dependence in Thermal Conductivity and Aerodynamic Roughness Length Estimates on a Debris‐covered Glacier.” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 130, no. 6, e2025JF008360, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2025jf008360\">10.1029/2025jf008360</a>.","ama":"Melo Velasco JV, Miles E, McCarthy M, et al. Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. <i>Journal of Geophysical Research: Earth Surface</i>. 2025;130(6). doi:<a href=\"https://doi.org/10.1029/2025jf008360\">10.1029/2025jf008360</a>","ista":"Melo Velasco JV, Miles E, McCarthy M, Shaw T, Fyffe CL, Fontrodona-Bach A, Pellicciotti F. 2025. Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. Journal of Geophysical Research: Earth Surface. 130(6), e2025JF008360.","apa":"Melo Velasco, J. V., Miles, E., McCarthy, M., Shaw, T., Fyffe, C. L., Fontrodona-Bach, A., &#38; Pellicciotti, F. (2025). Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier. <i>Journal of Geophysical Research: Earth Surface</i>. Wiley. <a href=\"https://doi.org/10.1029/2025jf008360\">https://doi.org/10.1029/2025jf008360</a>","short":"J.V. Melo Velasco, E. Miles, M. McCarthy, T. Shaw, C.L. Fyffe, A. Fontrodona-Bach, F. Pellicciotti, Journal of Geophysical Research: Earth Surface 130 (2025).","ieee":"J. V. Melo Velasco <i>et al.</i>, “Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier,” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 130, no. 6. Wiley, 2025."},"file":[{"date_created":"2025-06-24T06:27:34Z","access_level":"open_access","file_name":"2025_JGREarthSurface_MeloVelasco.pdf","file_size":3949928,"file_id":"19886","relation":"main_file","checksum":"ca91541516c71d240321630ca42b4dc4","success":1,"creator":"dernst","date_updated":"2025-06-24T06:27:34Z","content_type":"application/pdf"}],"isi":1,"external_id":{"isi":["001508794200001"]},"publication":"Journal of Geophysical Research: Earth Surface","day":"15","scopus_import":"1","type":"journal_article","title":"Method dependence in thermal conductivity and aerodynamic roughness length estimates on a debris‐covered glacier","oa_version":"Published Version","date_published":"2025-06-15T00:00:00Z","quality_controlled":"1","month":"06","intvolume":"       130","date_updated":"2025-09-30T13:42:28Z","publication_status":"published","_id":"19878","article_number":"e2025JF008360","doi":"10.1029/2025jf008360","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","status":"public","ddc":["550"],"language":[{"iso":"eng"}],"year":"2025","author":[{"last_name":"Melo Velasco","id":"2611dec0-b9c6-11ed-9bea-a81c2b17a549","first_name":"Juan Vicente","full_name":"Melo Velasco, Juan Vicente"},{"last_name":"Miles","first_name":"Evan","full_name":"Miles, Evan"},{"full_name":"McCarthy, Michael","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","last_name":"McCarthy"},{"full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","last_name":"Shaw"},{"full_name":"Fyffe, Catriona Louise","first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","last_name":"Fyffe"},{"full_name":"Fontrodona-Bach, Adrià","first_name":"Adrià","last_name":"Fontrodona-Bach","id":"f06891fd-9f42-11ee-8632-a20971c43046"},{"orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"}],"corr_author":"1","department":[{"_id":"FrPe"}],"abstract":[{"lang":"eng","text":"Rock debris partially covers glaciers worldwide, with varying extents and distributions, and controls sub‐debris melt rates by modifying energy transfer from the atmosphere to the ice. Two key physical properties controlling this energy exchange are thermal conductivity (k) and aerodynamic roughness length (z0). Accurate representation of these properties in energy‐balance models is critical for understanding climate‐glacier interactions and predicting the behavior of debris‐covered glaciers. However, k and z0 have been derived at very few sites from limited local measurements, using different approaches, and most model applications rely on values reported from these few sites and studies. We derive k and z0 using established and modified approaches from data at three locations on Pirámide Glacier in the central Chilean Andes. By comparing methods and evaluating melt simulated with an energy‐balance model, we reveal substantial differences between approaches. These lead to discrepancies between ice melt from energy‐balance simulations and observed data, and highlight the impact of method choice on calculated ice melt. Optimizing k against measured melt appears a viable approach to constrain melt simulations. Determining z0 seems less critical, as it has a smaller impact on total melt. Profile aerodynamic method measurements for estimating z0, despite higher costs, are independent of ice melt calculations. The large, unexpected differences between methods indicate a substantial knowledge gap. The fact that field‐derived k and z0 fail to work well in energy‐balance models, suggests that model values represent bulk properties distinct from theoretical field measurements. Addressing this gap is essential for improving glacier melt predictions."}],"acknowledgement":"This project received funding from the Swiss National Science Foundation (Grant 204322, project “REsolving the thickNess Of debris on Earth's glacIers and its Rate of change,” RENOIR). We thank Lars Groeneveld, Diego Hernández, Alonso Mejías, Gabriela Reyes and Gabriela Tala for their support during fieldwork. Open access funding provided by Institute of Science and Technology Austria/KEMÖ.","issue":"6","volume":130,"publication_identifier":{"issn":["2169-9003"],"eissn":["2169-9011"]},"article_type":"original","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","oa":1,"publisher":"Wiley","date_created":"2025-06-23T13:54:01Z","file_date_updated":"2025-06-24T06:27:34Z"},{"oa_version":"Published Version","scopus_import":"1","type":"journal_article","title":"Precoloring extension in planar near-Eulerian-triangulations","external_id":{"arxiv":["2312.13061"],"isi":["001443061400001"]},"day":"01","publication":"European Journal of Combinatorics","citation":{"chicago":"Dvořák, Zdeněk, Benjamin Moore, Michaela Seifrtová, and Robert Šámal. “Precoloring Extension in Planar Near-Eulerian-Triangulations.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">https://doi.org/10.1016/j.ejc.2025.104138</a>.","ama":"Dvořák Z, Moore B, Seifrtová M, Šámal R. Precoloring extension in planar near-Eulerian-triangulations. <i>European Journal of Combinatorics</i>. 2025;127. doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">10.1016/j.ejc.2025.104138</a>","mla":"Dvořák, Zdeněk, et al. “Precoloring Extension in Planar Near-Eulerian-Triangulations.” <i>European Journal of Combinatorics</i>, vol. 127, 104138, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">10.1016/j.ejc.2025.104138</a>.","ista":"Dvořák Z, Moore B, Seifrtová M, Šámal R. 2025. Precoloring extension in planar near-Eulerian-triangulations. European Journal of Combinatorics. 127, 104138.","short":"Z. Dvořák, B. Moore, M. Seifrtová, R. Šámal, European Journal of Combinatorics 127 (2025).","apa":"Dvořák, Z., Moore, B., Seifrtová, M., &#38; Šámal, R. (2025). Precoloring extension in planar near-Eulerian-triangulations. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2025.104138\">https://doi.org/10.1016/j.ejc.2025.104138</a>","ieee":"Z. Dvořák, B. Moore, M. Seifrtová, and R. Šámal, “Precoloring extension in planar near-Eulerian-triangulations,” <i>European Journal of Combinatorics</i>, vol. 127. Elsevier, 2025."},"file":[{"content_type":"application/pdf","date_updated":"2025-06-24T06:33:30Z","file_id":"19887","relation":"main_file","checksum":"8b3585df45b25091fba9bee9854b7d01","success":1,"creator":"dernst","date_created":"2025-06-24T06:33:30Z","access_level":"open_access","file_name":"2025_EuropJournCombinatorics_Dvorak.pdf","file_size":564203}],"isi":1,"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","article_number":"104138","doi":"10.1016/j.ejc.2025.104138","quality_controlled":"1","month":"06","intvolume":"       127","date_updated":"2025-09-30T13:42:59Z","publication_status":"published","_id":"19879","date_published":"2025-06-01T00:00:00Z","corr_author":"1","department":[{"_id":"MaKw"}],"language":[{"iso":"eng"}],"year":"2025","author":[{"last_name":"Dvořák","first_name":"Zdeněk","full_name":"Dvořák, Zdeněk"},{"id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","last_name":"Moore","first_name":"Benjamin","full_name":"Moore, Benjamin"},{"first_name":"Michaela","last_name":"Seifrtová","full_name":"Seifrtová, Michaela"},{"full_name":"Šámal, Robert","first_name":"Robert","last_name":"Šámal"}],"ddc":["510"],"status":"public","oa":1,"publisher":"Elsevier","date_created":"2025-06-23T13:54:46Z","file_date_updated":"2025-06-24T06:33:30Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":127,"publication_identifier":{"issn":["0195-6698"]},"OA_place":"publisher","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We consider the 4-precoloring extension problem in planar near-Eulerian- triangulations, i.e., plane graphs where all faces except possibly for the outer one have length three, all vertices not incident with the outer face have even degree, and exactly the vertices incident with the outer face are precolored. We give a necessary topological condition for the precoloring to extend, and give a complete characterization when the outer face has length at most five and when all vertices of the outer face have odd degree and are colored using only three colors."}],"acknowledgement":"Supported by project 22-17398S (Flows and cycles in graphs on surfaces) of Czech Science Foundation. An extended abstract appeared in Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications (EUROCOMB’23)","arxiv":1},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","OA_place":"publisher","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"volume":162,"issue":"23","arxiv":1,"acknowledgement":"We thank Artem Volosniev, Narcis Avarvari, Georgios Koutentakis, Sandro Wimberger, and Binghai Yan for useful discussions. R.A. received funding from the Austrian Academy of Science ÖWA, Grant No. PR1029OEAW03. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862-NeqMolRot.","abstract":[{"lang":"eng","text":"We investigate quantum transport in a two-dimensional electron system coupled to a chiral molecular potential, demonstrating how molecular chirality and orientation affect charge and spin transport properties. We propose a minimal model for realizing true chiral symmetry breaking on a magnetized surface, with a crucial role played by the tilt angle of the molecular dipole with respect to the surface. For non-zero tilting, we show that the Hall response exhibits clear signatures of chirality-induced effects, in both charge- and spin-resolved observables. Concerning the former, tilted enantiomers produce asymmetric Hall conductances and, even more remarkably, the persistence of this feature in the absence of spin–orbit coupling (SOC) signals how the enantiospecific charge response results from electron scattering off the molecular potential. Concerning spin-resolved observables where SOC plays a relevant role, we reveal that chiral symmetry breaking is crucial in enabling spin-flipping processes."}],"file_date_updated":"2025-06-23T14:03:30Z","date_created":"2025-06-23T13:55:28Z","oa":1,"publisher":"AIP Publishing","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"},{"name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862"},{"_id":"8fa7db46-16d5-11f0-9cad-917600954daf","grant_number":"12078","name":"Polarons in Lead Halide Perovskites"}],"ddc":["530"],"status":"public","department":[{"_id":"MiLe"}],"corr_author":"1","author":[{"full_name":"Al Hyder, Ragheed","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto"}],"language":[{"iso":"eng"}],"year":"2025","_id":"19880","date_updated":"2025-09-30T13:40:55Z","publication_status":"published","month":"06","intvolume":"       162","quality_controlled":"1","date_published":"2025-06-21T00:00:00Z","ec_funded":1,"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","doi":"10.1063/5.0271155","article_number":"234106","publication":"The Journal of Chemical Physics","day":"21","external_id":{"isi":["001512872900010"],"pmid":["40526561"],"arxiv":["2503.14124"]},"isi":1,"file":[{"date_updated":"2025-06-23T14:03:30Z","content_type":"application/pdf","access_level":"open_access","file_name":"2025_JourChemicalPhysics_AlHyder.pdf","date_created":"2025-06-23T14:03:30Z","file_size":7202681,"file_id":"19881","relation":"main_file","checksum":"e278631d949657baa9d5309dad5f4b77","creator":"dernst","success":1}],"citation":{"ista":"Al Hyder R, Lemeshko M, Cappellaro A. 2025. Quantum transport in the presence of a chiral molecular potential. The Journal of Chemical Physics. 162(23), 234106.","ama":"Al Hyder R, Lemeshko M, Cappellaro A. Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. 2025;162(23). doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>","mla":"Al Hyder, Ragheed, et al. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23, 234106, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>.","chicago":"Al Hyder, Ragheed, Mikhail Lemeshko, and Alberto Cappellaro. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>.","ieee":"R. Al Hyder, M. Lemeshko, and A. Cappellaro, “Quantum transport in the presence of a chiral molecular potential,” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23. AIP Publishing, 2025.","apa":"Al Hyder, R., Lemeshko, M., &#38; Cappellaro, A. (2025). Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>","short":"R. Al Hyder, M. Lemeshko, A. Cappellaro, The Journal of Chemical Physics 162 (2025)."},"oa_version":"Published Version","pmid":1,"type":"journal_article","title":"Quantum transport in the presence of a chiral molecular potential","scopus_import":"1"},{"article_processing_charge":"No","file_date_updated":"2025-06-25T07:11:52Z","date_created":"2025-06-24T06:56:03Z","oa":1,"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}],"doi":"10.15479/AT:ISTA:19885","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19885","date_updated":"2025-07-01T07:19:26Z","month":"06","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"acknowledgement":"The authors would like to thank Barnaby van Straaten, Jonas Schuff, Daniel Jirovec and Hanifa Tidjani for fruitful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. G.K. acknowledges support from the NOMIS Foundation, the HORIZON-RIA (project no. 101069515) and the FWF Projects (DOIs: 10.55776/F86 and 10.55776/I5060). N.A. acknowledges support from the European Research Council (grant agreement 948932), and the Royal Society (grant no. URF/R1/191150). This project received support from the US Army Research Office (ARO) under Award No. W911NF-24-2-0043. C.C. acknowledges support from the UKRI Doctoral Training Partnership related to EP/W524311/1 (project ref. 2887634).","date_published":"2025-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"This .zip file contains the data to reproduce the figures and supplementary figures of \"Automated All-RF Tuning for Spin Qubit Readout and Control\" by Cornelius Carlsson and Jaime Saez-Mollejo et al."}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"corr_author":"1","oa_version":"Published Version","author":[{"first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime"}],"type":"research_data","title":"Automated All-RF Tuning for Spin Qubit Readout and Control","year":"2025","day":"01","ddc":["530"],"file":[{"checksum":"eff1ae9e46599fdfab8da00a2ca3c289","relation":"main_file","file_id":"19893","creator":"jsaezmol","success":1,"access_level":"open_access","file_name":"DatasetsPaper.zip","date_created":"2025-06-24T15:14:13Z","file_size":3404814792,"content_type":"application/x-zip-compressed","date_updated":"2025-06-24T15:14:13Z"},{"date_created":"2025-06-25T07:11:52Z","access_level":"open_access","file_name":"README.txt","file_size":622,"file_id":"19899","checksum":"21840ceac04d677a799b8e5bd919804f","relation":"main_file","creator":"jsaezmol","success":1,"date_updated":"2025-06-25T07:11:52Z","content_type":"text/plain"}],"status":"public","citation":{"short":"J. 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Automated All-RF Tuning for Spin Qubit Readout and Control. 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>","ista":"Saez Mollejo J. 2025. Automated All-RF Tuning for Spin Qubit Readout and Control, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19885\">10.15479/AT:ISTA:19885</a>."},"contributor":[{"first_name":"Cornelius","last_name":"Carlsson","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Fedele","first_name":"Federico "},{"contributor_type":"researcher","last_name":"Calcaterra","first_name":"Stefano"},{"contributor_type":"researcher","last_name":"Chrastina","first_name":" Daniel "},{"contributor_type":"researcher","last_name":"Isella","first_name":"Giovanni "},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0001-8342-202X"},{"first_name":"Natalia","contributor_type":"researcher","last_name":"Ares"}]},{"file":[{"date_updated":"2025-06-27T07:35:29Z","content_type":"video/x-msvideo","file_name":"Supplementary Movie 1) in vivo time lapse microscopy of 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Files for ‘Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>.","chicago":"Springstein, Benjamin L. “Files for ‘Evolutionary Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cyanobacterial Cell Shape.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">https://doi.org/10.15479/AT:ISTA:19915</a>.","ama":"Springstein BL. Files for “Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>","mla":"Springstein, Benjamin L. <i>Files for “Evolutionary Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cyanobacterial Cell Shape.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19915\">10.15479/AT:ISTA:19915</a>.","short":"B.L. Springstein, (2025).","apa":"Springstein, B. L. (2025). Files for “Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19915\">https://doi.org/10.15479/AT:ISTA:19915</a>","ieee":"B. L. Springstein, “Files for ‘Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape.’” Institute of Science and Technology Austria, 2025."},"contributor":[{"contributor_type":"project_leader","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","last_name":"Springstein","first_name":"Benjamin L","orcid":"0000-0002-3461-5391"},{"first_name":"Manjunath","contributor_type":"researcher","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor"},{"first_name":"Daniela","contributor_type":"researcher","last_name":"Megrian"},{"first_name":"Roman","last_name":"Hajdu","id":"ffab949d-133f-11ed-8f02-94de21ace503","contributor_type":"researcher"},{"last_name":"Hanke","contributor_type":"researcher","first_name":"Dustin M"},{"contributor_type":"researcher","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","contributor_type":"supervisor"}],"status":"public","day":"27","type":"research_data","title":"Files for \"Evolutionary repurposing of a DNA segregation machinery into a cytoskeletal system controlling cyanobacterial cell shape\"","author":[{"first_name":"Benjamin L","last_name":"Springstein","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391"}],"year":"2025","department":[{"_id":"MaLo"}],"corr_author":"1","oa_version":"None","acknowledgement":"We thank all members of the Martin Loose lab at ISTA for helpful discussions and Marko Kojic for critical reading of the manuscript. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp) and the Electron Microscopy Facility (EMF), as well as the Lab Support Facility (LSF). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No.101034413 awarded to BLS as well as an ERC grant (ActinID, 101076260) from the European Union awarded to FKMS. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.\r\n\r\nWe are grateful for Antonia Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids as well as cyanobacterial strains. Likewise, we would like to thank Tal Dagan and Fabian Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions.\r\n\r\nWe would further like to express our gratitude to Nicolas Sapay and Alexis Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins. Finally, we also want to thank Jesse Hansen for advice in cryo-EM data processing","date_published":"2025-06-27T00:00:00Z","ec_funded":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"19915","date_updated":"2025-07-02T08:25:37Z","month":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","doi":"10.15479/AT:ISTA:19915","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"name":"A molecular atlas of Actin filament IDentities in the cell motility machinery","_id":"bd980d18-d553-11ed-ba76-ceaa645c97eb","grant_number":"101076260"}],"article_processing_charge":"No","file_date_updated":"2025-07-02T08:10:21Z","date_created":"2025-06-27T07:34:52Z","publisher":"Institute of Science and Technology Austria","oa":1},{"date_published":"2025-09-01T00:00:00Z","quality_controlled":"1","intvolume":"       222","month":"09","date_updated":"2025-12-30T09:00:42Z","publication_status":"published","_id":"19928","article_number":"e20240109","doi":"10.1084/jem.20240109","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","citation":{"ieee":"R. Gawish <i>et al.</i>, “Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis,” <i>Journal of Experimental Medicine</i>, vol. 222, no. 9. Rockefeller University Press, 2025.","apa":"Gawish, R., Varada, R., Deckert, F., Hladik, A., Steinbichl, L., Cimatti, L., … Vesely, C. (2025). Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. <i>Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20240109\">https://doi.org/10.1084/jem.20240109</a>","short":"R. Gawish, R. Varada, F. Deckert, A. Hladik, L. Steinbichl, L. Cimatti, K. Milanovic, M. Jain, N. Torgasheva, A. Tanzer, K. De Paepe, T. Van De Wiele, B. Hausmann, M. Lang, M. Pechhacker, N. Ibrahim, I. de Vries, C. Brostjan, M.K. Sixt, C. Gasche, L. Boon, D. Berry, M.F. Jantsch, F.C. Pereira, C. Vesely, Journal of Experimental Medicine 222 (2025).","ista":"Gawish R, Varada R, Deckert F, Hladik A, Steinbichl L, Cimatti L, Milanovic K, Jain M, Torgasheva N, Tanzer A, De Paepe K, Van De Wiele T, Hausmann B, Lang M, Pechhacker M, Ibrahim N, de Vries I, Brostjan C, Sixt MK, Gasche C, Boon L, Berry D, Jantsch MF, Pereira FC, Vesely C. 2025. Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. Journal of Experimental Medicine. 222(9), e20240109.","mla":"Gawish, Riem, et al. “Filamin A Editing in Myeloid Cells Reduces Intestinal Inflammation and Protects from Colitis.” <i>Journal of Experimental Medicine</i>, vol. 222, no. 9, e20240109, Rockefeller University Press, 2025, doi:<a href=\"https://doi.org/10.1084/jem.20240109\">10.1084/jem.20240109</a>.","ama":"Gawish R, Varada R, Deckert F, et al. Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis. <i>Journal of Experimental Medicine</i>. 2025;222(9). doi:<a href=\"https://doi.org/10.1084/jem.20240109\">10.1084/jem.20240109</a>","chicago":"Gawish, Riem, Rajagopal Varada, Florian Deckert, Anastasiya Hladik, Linda Steinbichl, Laura Cimatti, Katarina Milanovic, et al. “Filamin A Editing in Myeloid Cells Reduces Intestinal Inflammation and Protects from Colitis.” <i>Journal of Experimental Medicine</i>. Rockefeller University Press, 2025. <a href=\"https://doi.org/10.1084/jem.20240109\">https://doi.org/10.1084/jem.20240109</a>."},"file":[{"creator":"dernst","success":1,"file_id":"20899","checksum":"708d61fb8cf1d83ee1e33ddcfde0857e","relation":"main_file","file_size":9349311,"access_level":"open_access","file_name":"2025_JEM_Gawish.pdf","date_created":"2025-12-30T09:00:04Z","content_type":"application/pdf","date_updated":"2025-12-30T09:00:04Z"}],"isi":1,"external_id":{"isi":["001502896900001"],"pmid":["40471139"]},"day":"01","publication":"Journal of Experimental Medicine","scopus_import":"1","title":"Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis","type":"journal_article","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation."}],"acknowledgement":"Sequencing was performed by the Vienna BioCenter Core Facilities (Medical University of Vienna Core Facility) and the Biomedical Sequencing Facility at CeMM, Vienna. Cell sorting and flow cytometry were performed at the Core Facility Flow Cytometry and Imaging (Medical University of Vienna). We thank Jasmin Schwarz, Gudrun Kohl, Petra Pjevac, and Joana Seneca Silva from the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna for assisting with amplicon and metagenomic sequencing, as well as repositing of sequencing data. We thank Sophia Derdak and Michael Schuster for initial data analysis, Robert Vilvoi and Stephan Hemm for animal handling, Marcel Kertesz for mouse genotyping, and Salwan Roumaia for next generation sequencing sample preparation. Treatment schemes and graphical abstracts were created with https://BioRender.com.\r\n\r\nThis work was supported by the Austrian Science Fund, grant number ZK 57-B28 to C. Vesely, R. Gawish, and F.C. Pereira; grant number V 1025-B to R. Gawish; grant number DOC32-B28 to R. Varada and M.F. Jantsch; and F8007 and P32678 to M.F. Jantsch. Open Access funding provided by Medical University of Vienna.","issue":"9","volume":222,"publication_identifier":{"eissn":["1540-9538"],"issn":["0022-1007"]},"OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Rockefeller University Press","oa":1,"date_created":"2025-06-29T22:01:15Z","file_date_updated":"2025-12-30T09:00:04Z","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"year":"2025","author":[{"first_name":"Riem","last_name":"Gawish","full_name":"Gawish, Riem"},{"full_name":"Varada, Rajagopal","first_name":"Rajagopal","last_name":"Varada"},{"full_name":"Deckert, Florian","last_name":"Deckert","first_name":"Florian"},{"first_name":"Anastasiya","last_name":"Hladik","full_name":"Hladik, Anastasiya"},{"first_name":"Linda","last_name":"Steinbichl","full_name":"Steinbichl, Linda"},{"first_name":"Laura","last_name":"Cimatti","full_name":"Cimatti, Laura"},{"first_name":"Katarina","last_name":"Milanovic","full_name":"Milanovic, Katarina"},{"full_name":"Jain, Mamta","first_name":"Mamta","last_name":"Jain"},{"last_name":"Torgasheva","first_name":"Natalya","full_name":"Torgasheva, Natalya"},{"first_name":"Andrea","last_name":"Tanzer","full_name":"Tanzer, Andrea"},{"last_name":"De Paepe","first_name":"Kim","full_name":"De Paepe, Kim"},{"full_name":"Van De Wiele, Tom","first_name":"Tom","last_name":"Van De Wiele"},{"first_name":"Bela","last_name":"Hausmann","full_name":"Hausmann, Bela"},{"last_name":"Lang","first_name":"Michaela","full_name":"Lang, Michaela"},{"last_name":"Pechhacker","first_name":"Martin","full_name":"Pechhacker, Martin"},{"full_name":"Ibrahim, Nahla","first_name":"Nahla","last_name":"Ibrahim"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"last_name":"Brostjan","first_name":"Christine","full_name":"Brostjan, Christine"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Gasche, Christoph","first_name":"Christoph","last_name":"Gasche"},{"full_name":"Boon, Louis","first_name":"Louis","last_name":"Boon"},{"full_name":"Berry, David","last_name":"Berry","first_name":"David"},{"first_name":"Michael F.","last_name":"Jantsch","full_name":"Jantsch, Michael F."},{"last_name":"Pereira","first_name":"Fatima C.","full_name":"Pereira, Fatima C."},{"last_name":"Vesely","first_name":"Cornelia","full_name":"Vesely, Cornelia"}],"department":[{"_id":"MiSi"}]},{"volume":698,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Context. The observed Lyman-alpha (Lyα) line profile is a convolution of the complex Lyα radiative transfer taking place in the interstellar, circumgalactic, and intergalactic media (ISM, CGM, and IGM, respectively). Discerning the different components of the Lyα line is crucial in order to use it as a probe of galaxy formation or the evolution of the IGM.\r\n\r\nAims. We aim to present the second version of zELDA (redshift Estimator for Line profiles of Distant Lyman-Alpha emitters), an open-source Python module focused on modelling and fitting observed Lyα line profiles. This new version of zELDA focuses on disentangling the galactic from the IGM effects.\r\n\r\nMethods. We built realistic Lyα line profiles that include the ISM and IGM contributions by combining the Monte Carlo radiative-transfer simulations for the so-called shell model (ISM) and IGM transmission curves generated from TNG100. We used these mock line profiles to train different artificial neural networks. These use the observed spectrum as input and the outflow parameters of the best fitting ‘shell model’ as output along with the redshift and Lyα emission IGM escape fraction of the source.\r\n\r\nResults. We measured the accuracy of zELDA on mock Lyα line profiles. We find that zELDA is capable of reconstructing the ISM emerging Lyα line profile with high levels of accuracy (Kolmogórov-Smirnov<0.1) for 95% of the cases for HST/COS-like observations and 80% for MUSE-WIDE-like observations. zELDA is able to measure the IGM transmission with typical uncertainties below 10% for HST/COS and MUSE-WIDE data.\r\n\r\nConclusions. This work represents a step forward in the high-precision reconstruction of IGM-attenuated Lyα line profiles. zELDA allows the disentanglement of the galactic and IGM contribution shaping the Lyα line shape and thus allows us to use Lyα as a tool to study galaxy and ISM evolution.","lang":"eng"}],"acknowledgement":"The authors acknowledge the financial support from the MICIU with funding from the European Union NextGenerationEU and Generalitat Valenciana in the call Programa de Planes Complementarios de I+D+i (PRTR 2022) Project (VAL-JPAS), reference ASFAE/2022/025. This work is part of the research Project PID2023-149420NB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU. This work is also supported by the project of excellence PROMETEO CIPROM/2023/21 of the Conselleria de Educación, Universidades y Empleo (Generalitat Valenciana). MG thanks the Max Planck Society for support through the Max Planck Research Group. DS acknowledges the support by the Tsinghua Shui Mu Scholarship, funding of the National Key R&D Program of China (grant no. 2023YFA1605600), the science research grants from the China Manned Space Project with no. CMS-CSST2021-A05, and the Tsinghua University Initiative Scientific Research Program (no. 20223080023). This research made use of matplotlib, a Python library for publication quality graphics (Hunter 2007), NumPy (Harris et al. 2020) and SciPy (Virtanen et al. 2020).","arxiv":1,"oa":1,"publisher":"EDP Sciences","date_created":"2025-06-29T22:01:15Z","file_date_updated":"2025-06-30T08:28:40Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["520"],"status":"public","department":[{"_id":"JoMa"}],"language":[{"iso":"eng"}],"year":"2025","author":[{"full_name":"Gurung-López, Siddhartha","last_name":"Gurung-López","first_name":"Siddhartha"},{"first_name":"Chris","last_name":"Byrohl","full_name":"Byrohl, Chris"},{"last_name":"Gronke","first_name":"Max","full_name":"Gronke, Max"},{"last_name":"Spinoso","first_name":"Daniele","full_name":"Spinoso, Daniele"},{"orcid":"0000-0001-5586-6950","full_name":"Torralba Torregrosa, Alberto","id":"018f0249-0e87-11f0-b167-cbce08fbd541","last_name":"Torralba Torregrosa","first_name":"Alberto"},{"last_name":"Fernández-Soto","first_name":"Alberto","full_name":"Fernández-Soto, Alberto"},{"full_name":"Arnalte-Mur, Pablo","last_name":"Arnalte-Mur","first_name":"Pablo"},{"full_name":"Martínez, Vicent J.","last_name":"Martínez","first_name":"Vicent J."}],"quality_controlled":"1","month":"06","intvolume":"       698","publication_status":"published","date_updated":"2026-02-16T12:11:56Z","_id":"19929","date_published":"2025-06-01T00:00:00Z","article_processing_charge":"No","OA_type":"diamond","article_number":"A139","doi":"10.1051/0004-6361/202453547","external_id":{"isi":["001507317300003"],"arxiv":["2501.04077"]},"day":"01","publication":"Astronomy & Astrophysics","citation":{"ieee":"S. Gurung-López <i>et al.</i>, “zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025.","apa":"Gurung-López, S., Byrohl, C., Gronke, M., Spinoso, D., Torralba Torregrosa, A., Fernández-Soto, A., … Martínez, V. J. (2025). zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202453547\">https://doi.org/10.1051/0004-6361/202453547</a>","short":"S. Gurung-López, C. Byrohl, M. Gronke, D. Spinoso, A. Torralba Torregrosa, A. Fernández-Soto, P. Arnalte-Mur, V.J. Martínez, Astronomy &#38; Astrophysics 698 (2025).","ista":"Gurung-López S, Byrohl C, Gronke M, Spinoso D, Torralba Torregrosa A, Fernández-Soto A, Arnalte-Mur P, Martínez VJ. 2025. zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. Astronomy &#38; Astrophysics. 698, A139.","ama":"Gurung-López S, Byrohl C, Gronke M, et al. zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202453547\">10.1051/0004-6361/202453547</a>","mla":"Gurung-López, Siddhartha, et al. “ZELDA II: Reconstruction of Galactic Lyman-Alpha Spectra Attenuated by the Intergalactic Medium Using Neural Networks.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A139, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202453547\">10.1051/0004-6361/202453547</a>.","chicago":"Gurung-López, Siddhartha, Chris Byrohl, Max Gronke, Daniele Spinoso, Alberto Torralba Torregrosa, Alberto Fernández-Soto, Pablo Arnalte-Mur, and Vicent J. Martínez. “ZELDA II: Reconstruction of Galactic Lyman-Alpha Spectra Attenuated by the Intergalactic Medium Using Neural Networks.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202453547\">https://doi.org/10.1051/0004-6361/202453547</a>."},"file":[{"content_type":"application/pdf","date_updated":"2025-06-30T08:28:40Z","creator":"dernst","success":1,"file_id":"19933","relation":"main_file","checksum":"a50a817b72f03534c6a867035b51e433","file_size":5758102,"date_created":"2025-06-30T08:28:40Z","file_name":"2025_AstronomyAstrophysics_GurungLopez.pdf","access_level":"open_access"}],"isi":1,"oa_version":"Published Version","scopus_import":"1","type":"journal_article","title":"zELDA II: Reconstruction of galactic Lyman-alpha spectra attenuated by the intergalactic medium using neural networks"},{"file_date_updated":"2025-06-30T08:22:08Z","oa":1,"publisher":"EDP Sciences","date_created":"2025-06-29T22:01:15Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"volume":698,"acknowledgement":"We acknowledges support from the INAF Large Grant for Extragalactic Surveys with JWST and from the PRIN 2022 MUR project 2022CB3PJ3 – First Light And Galaxy aSsembly (FLAGS) funded by the European Union – Next Generation EU. PS acknowledges INAF Mini Grant 2022 “The evolution of passive galaxies through cosmic time”. Part of the research activities described in this paper were carried out with the contribution of the Next Generation EU funds within the National Recovery and Resilience Plan (PNRR), Mission 4 – Education and Research, Component 2 – From Research to Business (M4C2), Investment Line 3.1 – Strengthening and creation of Research Infrastructures, Project IR0000034 – “STILES – Strengthening the Italian Leadership in ELT and SKA”. RA acknowledges support of Grant project PID2023-147386NB-I00 funded by MICIU/AEI/10.13039/501100011033 and by ERDF/EU, and the Severo Ochoa grant CEX2021-001131-S funded by MCIN/AEI/10.13039/50110001103.","arxiv":1,"abstract":[{"text":"We present an analysis of the UV continuum slope, β, using a sample of 726 galaxies with z > 4, selected from a mixture of JWST ERS, GTO, and GO observational programs. We considered only spectroscopic data obtained with the low-resolution (R ∼ 30 − 300) PRISM/CLEAR NIRSpec configuration. Studying the correlation between β and MUV, we find an overall decreasing trend, described by β = ( − 0.055 ± 0.017)MUV + ( − 2.98 ± 0.34). This is consistent with previous studies, where brighter galaxies show redder β values. However, when analyzing the trend in separate redshift bins, we find that at high redshift the relation becomes much flatter and is consistent with a flat slope within 1σ. Furthermore, we find that β tends to decrease with redshift, following β = ( − 0.075 ± 0.010)z + ( − 1.496 ± 0.056). This is consistent with most recent results showing a steepening of the spectra at higher z. We selected a sample of galaxies with extremely blue slopes (i.e., β < −2.6). Such slopes are steeper than predicted by stellar evolution models – even for dust-free, young, metal-poor populations – when the contribution of nebular emission is included. We selected 44 extremely blue galaxies (XBGs) and investigated the possible physical origin of their steep slopes by comparing them to a subsample of redder galaxies (matched in Δz = ±0.5 and ΔMUV = ±0.2). We find that XBGs have younger stellar populations, stronger ionization fields, lower dust attenuation, and lower but not pristine metallicity (∼10% Z⊙) compared to red galaxies. However, these properties alone cannot explain the extreme β values. Using indirect inference of Lyman continuum escape with the most recent models, we estimated the escape fraction fesc > 10% in at least 25% of the XBGs, whereas all the red sources exhibit much lower fesc values. A reduced nebular continuum contribution – resulting from either a high escape fraction or a bursty star formation history – is likely the origin of the extremely blue slopes.","lang":"eng"}],"department":[{"_id":"JoMa"}],"year":"2025","language":[{"iso":"eng"}],"author":[{"full_name":"Dottorini, D.","first_name":"D.","last_name":"Dottorini"},{"last_name":"Calabrò","first_name":"A.","full_name":"Calabrò, A."},{"last_name":"Pentericci","first_name":"L.","full_name":"Pentericci, L."},{"full_name":"Mascia, Sara","first_name":"Sara","last_name":"Mascia","id":"edaf889c-c7cd-11ef-ab1b-bb28c431bd29"},{"full_name":"Llerena, M.","last_name":"Llerena","first_name":"M."},{"full_name":"Napolitano, L.","first_name":"L.","last_name":"Napolitano"},{"last_name":"Santini","first_name":"P.","full_name":"Santini, P."},{"last_name":"Roberts-Borsani","first_name":"G.","full_name":"Roberts-Borsani, G."},{"full_name":"Castellano, M.","last_name":"Castellano","first_name":"M."},{"last_name":"Amorin","first_name":"R.","full_name":"Amorin, R."},{"last_name":"Dickinson","first_name":"M.","full_name":"Dickinson, M."},{"full_name":"Fontana, A.","first_name":"A.","last_name":"Fontana"},{"full_name":"Hathi, N.","last_name":"Hathi","first_name":"N."},{"last_name":"Hirschmann","first_name":"M.","full_name":"Hirschmann, M."},{"full_name":"Koekemoer, A. M.","first_name":"A. M.","last_name":"Koekemoer"},{"full_name":"Lucas, R. A.","last_name":"Lucas","first_name":"R. A."},{"first_name":"E.","last_name":"Merlin","full_name":"Merlin, E."},{"full_name":"Morales, A.","last_name":"Morales","first_name":"A."},{"last_name":"Pacucci","first_name":"F.","full_name":"Pacucci, F."},{"first_name":"S.","last_name":"Wilkins","full_name":"Wilkins, S."},{"last_name":"Arrabal Haro","first_name":"P.","full_name":"Arrabal Haro, P."},{"full_name":"Bagley, M.","last_name":"Bagley","first_name":"M."},{"last_name":"Finkelstein","first_name":"S. L.","full_name":"Finkelstein, S. L."},{"first_name":"J.","last_name":"Kartaltepe","full_name":"Kartaltepe, J."},{"full_name":"Papovich, C.","last_name":"Papovich","first_name":"C."},{"full_name":"Pirzkal, N.","first_name":"N.","last_name":"Pirzkal"}],"ddc":["520"],"status":"public","OA_type":"diamond","article_processing_charge":"No","article_number":"A234","doi":"10.1051/0004-6361/202453267","date_updated":"2026-02-16T12:11:39Z","publication_status":"published","_id":"19930","quality_controlled":"1","intvolume":"       698","month":"06","date_published":"2025-06-01T00:00:00Z","oa_version":"Published Version","title":"Evolution of the UV slope of galaxies at cosmic morning (z > 4): The properties of extremely blue galaxies","type":"journal_article","scopus_import":"1","publication":"Astronomy & Astrophysics","day":"01","external_id":{"isi":["001510826300019"],"arxiv":["2412.01623"]},"file":[{"file_size":2442076,"date_created":"2025-06-30T08:22:08Z","access_level":"open_access","file_name":"2025_AstronomyAstrophysics_Dottorini.pdf","creator":"dernst","success":1,"file_id":"19932","checksum":"100f897d468de9d0113277c870035b62","relation":"main_file","date_updated":"2025-06-30T08:22:08Z","content_type":"application/pdf"}],"isi":1,"citation":{"mla":"Dottorini, D., et al. “Evolution of the UV Slope of Galaxies at Cosmic Morning (z &#62; 4): The Properties of Extremely Blue Galaxies.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A234, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202453267\">10.1051/0004-6361/202453267</a>.","ama":"Dottorini D, Calabrò A, Pentericci L, et al. Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202453267\">10.1051/0004-6361/202453267</a>","chicago":"Dottorini, D., A. Calabrò, L. Pentericci, Sara Mascia, M. Llerena, L. Napolitano, P. Santini, et al. “Evolution of the UV Slope of Galaxies at Cosmic Morning (z &#62; 4): The Properties of Extremely Blue Galaxies.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202453267\">https://doi.org/10.1051/0004-6361/202453267</a>.","ista":"Dottorini D, Calabrò A, Pentericci L, Mascia S, Llerena M, Napolitano L, Santini P, Roberts-Borsani G, Castellano M, Amorin R, Dickinson M, Fontana A, Hathi N, Hirschmann M, Koekemoer AM, Lucas RA, Merlin E, Morales A, Pacucci F, Wilkins S, Arrabal Haro P, Bagley M, Finkelstein SL, Kartaltepe J, Papovich C, Pirzkal N. 2025. Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. Astronomy &#38; Astrophysics. 698, A234.","ieee":"D. Dottorini <i>et al.</i>, “Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025.","apa":"Dottorini, D., Calabrò, A., Pentericci, L., Mascia, S., Llerena, M., Napolitano, L., … Pirzkal, N. (2025). Evolution of the UV slope of galaxies at cosmic morning (z &#62; 4): The properties of extremely blue galaxies. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202453267\">https://doi.org/10.1051/0004-6361/202453267</a>","short":"D. Dottorini, A. Calabrò, L. Pentericci, S. Mascia, M. Llerena, L. Napolitano, P. Santini, G. Roberts-Borsani, M. Castellano, R. Amorin, M. Dickinson, A. Fontana, N. Hathi, M. Hirschmann, A.M. Koekemoer, R.A. Lucas, E. Merlin, A. Morales, F. Pacucci, S. Wilkins, P. Arrabal Haro, M. Bagley, S.L. Finkelstein, J. Kartaltepe, C. Papovich, N. Pirzkal, Astronomy &#38; Astrophysics 698 (2025)."}},{"article_number":"A227","doi":"10.1051/0004-6361/202554110","OA_type":"diamond","article_processing_charge":"No","date_published":"2025-06-01T00:00:00Z","date_updated":"2026-02-16T12:11:22Z","publication_status":"published","_id":"19931","quality_controlled":"1","month":"06","intvolume":"       698","type":"journal_article","title":"Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"19934","checksum":"567fa02a9791d489355ec75d02bb1cb9","relation":"main_file","success":1,"creator":"dernst","date_created":"2025-06-30T08:44:24Z","access_level":"open_access","file_name":"2025_AstronomyAstrophysics_Furtak.pdf","file_size":1835865,"content_type":"application/pdf","date_updated":"2025-06-30T08:44:24Z"}],"isi":1,"citation":{"chicago":"Furtak, Lukas J., Amy R. Secunda, Jenny E. Greene, Adi Zitrin, Ivo Labbé, Miriam Golubchik, Rachel Bezanson, et al. “Investigating Photometric and Spectroscopic Variability in the Multiply Imaged Little Red Dot A2744-QSO1.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202554110\">https://doi.org/10.1051/0004-6361/202554110</a>.","ama":"Furtak LJ, Secunda AR, Greene JE, et al. Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. <i>Astronomy &#38; Astrophysics</i>. 2025;698. doi:<a href=\"https://doi.org/10.1051/0004-6361/202554110\">10.1051/0004-6361/202554110</a>","mla":"Furtak, Lukas J., et al. “Investigating Photometric and Spectroscopic Variability in the Multiply Imaged Little Red Dot A2744-QSO1.” <i>Astronomy &#38; Astrophysics</i>, vol. 698, A227, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202554110\">10.1051/0004-6361/202554110</a>.","ista":"Furtak LJ, Secunda AR, Greene JE, Zitrin A, Labbé I, Golubchik M, Bezanson R, Kokorev V, Atek H, Brammer GB, Chemerynska I, Cutler SE, Dayal P, Feldmann R, Fujimoto S, Glazebrook K, Leja J, Ma Y, Matthee JJ, Naidu RP, Nelson EJ, Oesch PA, Pan R, Price SH, Suess KA, Wang B, Weaver JR, Whitaker KE. 2025. Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. Astronomy &#38; Astrophysics. 698, A227.","apa":"Furtak, L. J., Secunda, A. R., Greene, J. E., Zitrin, A., Labbé, I., Golubchik, M., … Whitaker, K. E. (2025). Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202554110\">https://doi.org/10.1051/0004-6361/202554110</a>","short":"L.J. Furtak, A.R. Secunda, J.E. Greene, A. Zitrin, I. Labbé, M. Golubchik, R. Bezanson, V. Kokorev, H. Atek, G.B. Brammer, I. Chemerynska, S.E. Cutler, P. Dayal, R. Feldmann, S. Fujimoto, K. Glazebrook, J. Leja, Y. Ma, J.J. Matthee, R.P. Naidu, E.J. Nelson, P.A. Oesch, R. Pan, S.H. Price, K.A. Suess, B. Wang, J.R. Weaver, K.E. Whitaker, Astronomy &#38; Astrophysics 698 (2025).","ieee":"L. J. Furtak <i>et al.</i>, “Investigating photometric and spectroscopic variability in the multiply imaged little red dot A2744-QSO1,” <i>Astronomy &#38; Astrophysics</i>, vol. 698. EDP Sciences, 2025."},"publication":"Astronomy & Astrophysics","day":"01","external_id":{"arxiv":["2502.07875"],"isi":["001510826300017"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","file_date_updated":"2025-06-30T08:44:24Z","publisher":"EDP Sciences","oa":1,"date_created":"2025-06-29T22:01:16Z","acknowledgement":"We would like to thank Xihan Ji, Hannah Übler, and Roberto Maiolino, for cordial and useful discussions. The BGU lensing group acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Israel Science Foundation Grant No. 864/23. P.D. warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. This work is based on observations obtained with the NASA/ESA/CSA JWST, namely programs GO-2756, -2561, -2883, -3538, -4111, and -3516, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. The spectroscopy products presented herein, from JWST program GO-2561, were retrieved from the Dawn JWST Archive (DJA). DJA is an initiative of the Cosmic Dawn Center (DAWN), which is funded by the Danish National Research Foundation under grant DNRF140. The data used in this work may be retrieved from the MAST archive at: http://dx.doi.org/10.17909/p7t7-te67. This work also makes use of the Center for Computational Astrophysics at the Flatiron Institute which is supported by the Simons Foundation. Support for JWST programs GO-2561, -4111, and -3516 was provided by NASA through grants from STScI. This research made use of Astropy, (http://www.astropy.org) a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018) and Photutils, an Astropy package for detection and photometry of astronomical sources (Bradley et al. 2024), as well as the packages NumPy (van der Walt et al. 2011), SciPy (Virtanen et al. 2020), Matplotlib (Hunter 2007), and the MAAT Astronomy and Astrophysics tools for MATLAB (Ofek 2014).","arxiv":1,"abstract":[{"lang":"eng","text":"JWST observations have uncovered a new population of red, compact objects at high redshifts dubbed “little red dots” (LRDs), which typically show broad emission lines and are thought to be dusty active galactic nuclei (AGNs). Some of their other features, however, challenge the AGN explanation, such as prominent Balmer breaks and extremely faint or even missing metal high-ionization lines, X-ray, or radio emission, including in deep stacks. Time variability is another robust test of AGN activity. Here, we exploit the z = 7.045 multiply imaged LRD A2744-QSO1, which offers a particularly unique test of variability due to lensing-induced time delays between the three images spanning 22 yr (2.7 yr in the rest-frame), to investigate its photometric and spectroscopic variability. We find the equivalent widths (EWs) of the broad Hα and Hβ lines, which are independent of magnification and other systematics, to exhibit significant variations, of up to 18 ± 3% for Hα and up to 22 ± 8% in Hβ, on a timescale of 875 d (2.4 yr) in the rest-frame. This suggests that A2744-QSO1 is indeed an AGN. We find no significant photometric variability beyond the limiting systematic uncertainties, so it currently cannot be determined whether the EW variations are due to line-flux or continuum variability. These results are consistent with a typical damped random walk variability model for an AGN such as A2744-QSO1 (MBH = 4 × 107 M⊙) given the sparse sampling of the light curve with the available data. Our results therefore support the AGN interpretation of this LRD, and highlight the need for further photometric and spectroscopic monitoring in order to build a detailed and reliable light curve."}],"OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":698,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"year":"2025","language":[{"iso":"eng"}],"author":[{"full_name":"Furtak, Lukas J.","last_name":"Furtak","first_name":"Lukas J."},{"full_name":"Secunda, Amy R.","first_name":"Amy R.","last_name":"Secunda"},{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"first_name":"Adi","last_name":"Zitrin","full_name":"Zitrin, Adi"},{"first_name":"Ivo","last_name":"Labbé","full_name":"Labbé, Ivo"},{"full_name":"Golubchik, Miriam","first_name":"Miriam","last_name":"Golubchik"},{"first_name":"Rachel","last_name":"Bezanson","full_name":"Bezanson, Rachel"},{"full_name":"Kokorev, Vasily","last_name":"Kokorev","first_name":"Vasily"},{"full_name":"Atek, Hakim","first_name":"Hakim","last_name":"Atek"},{"first_name":"Gabriel B.","last_name":"Brammer","full_name":"Brammer, Gabriel B."},{"full_name":"Chemerynska, Iryna","first_name":"Iryna","last_name":"Chemerynska"},{"first_name":"Sam E.","last_name":"Cutler","full_name":"Cutler, Sam E."},{"full_name":"Dayal, Pratika","last_name":"Dayal","first_name":"Pratika"},{"last_name":"Feldmann","first_name":"Robert","full_name":"Feldmann, Robert"},{"full_name":"Fujimoto, Seiji","first_name":"Seiji","last_name":"Fujimoto"},{"last_name":"Glazebrook","first_name":"Karl","full_name":"Glazebrook, Karl"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"full_name":"Ma, Yilun","first_name":"Yilun","last_name":"Ma"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"last_name":"Naidu","first_name":"Rohan P.","full_name":"Naidu, Rohan P."},{"full_name":"Nelson, Erica J.","last_name":"Nelson","first_name":"Erica J."},{"full_name":"Oesch, Pascal A.","first_name":"Pascal A.","last_name":"Oesch"},{"first_name":"Richard","last_name":"Pan","full_name":"Pan, Richard"},{"last_name":"Price","first_name":"Sedona H.","full_name":"Price, Sedona H."},{"last_name":"Suess","first_name":"Katherine A.","full_name":"Suess, Katherine A."},{"last_name":"Wang","first_name":"Bingjie","full_name":"Wang, Bingjie"},{"full_name":"Weaver, John R.","last_name":"Weaver","first_name":"John R."},{"full_name":"Whitaker, Katherine E.","last_name":"Whitaker","first_name":"Katherine E."}],"department":[{"_id":"JoMa"}],"status":"public","ddc":["520"]}]