[{"abstract":[{"lang":"eng","text":"We present the Red Unknowns: Bright Infrared Extragalactic Survey (RUBIES) providing JWST/NIRSpec spectroscopy of red sources selected across ∼150 arcmin2 from public JWST/NIRCam imaging in the UDS and EGS fields. The novel observing strategy of RUBIES offers a well-quantified selection function. The survey has been optimised to reach high (>70%) spectroscopic completeness for bright and red (F150W−F444W>2) sources that are very rare. To place these rare sources in context, we simultaneously observed a reference sample of the 23 using only the G395M disperser. The RUBIES data reveal a highly diverse population of red sources that span a broad redshift range (zspec∼1−9), with photometric redshift scatter and an outlier fraction that are three times higher than for similarly bright sources that are less red. This diversity is not apparent from the photometric spectral energy distributions (SEDs). Only spectroscopy reveals that the SEDs encompass a mixture of galaxies with dust-obscured star formation, extreme line emission, a lack of star formation indicating early quenching, and luminous active galactic nuclei. As a first demonstration of our broader selection function we compared the stellar masses and rest-frame U−V colours of the red sources and our reference sample. We find that the red sources are typically more massive (M*∼1010−11.5 M⊙) across all redshifts. However, we also find that the most massive systems span a wide range in U−V colour. We describe our data reduction procedure and data quality, and we publicly release the reduced RUBIES data and vetted spectroscopic redshifts of the first half of the survey through the DAWN JWST Archive."}],"fulldoi":"https://doi.org/10.1051/0004-6361/202452186","file_date_updated":"2025-06-03T09:25:49Z","OA_place":"publisher","day":"19","publication_status":"published","author":[{"full_name":"de Graaff, Anna","first_name":"Anna","last_name":"de Graaff"},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"first_name":"Zach","full_name":"Lewis, Zach","last_name":"Lewis"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"full_name":"Bezanson, Rachel","first_name":"Rachel","last_name":"Bezanson"},{"last_name":"Boogaard","full_name":"Boogaard, Leindert A.","first_name":"Leindert A."},{"last_name":"Cleri","full_name":"Cleri, Nikko J.","first_name":"Nikko J."},{"full_name":"Cooper, Olivia R.","first_name":"Olivia R.","last_name":"Cooper"},{"first_name":"Rashmi","full_name":"Gottumukkala, Rashmi","last_name":"Gottumukkala"},{"last_name":"Greene","full_name":"Greene, Jenny E.","first_name":"Jenny E."},{"last_name":"Hirschmann","full_name":"Hirschmann, Michaela","first_name":"Michaela"},{"last_name":"Hviding","first_name":"Raphael E.","full_name":"Hviding, Raphael E."},{"full_name":"Katz, Harley","first_name":"Harley","last_name":"Katz"},{"last_name":"Labbé","first_name":"Ivo","full_name":"Labbé, Ivo"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X"},{"last_name":"McConachie","full_name":"McConachie, Ian","first_name":"Ian"},{"last_name":"Miller","first_name":"Tim B.","full_name":"Miller, Tim B."},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"last_name":"Price","first_name":"Sedona H.","full_name":"Price, Sedona H."},{"last_name":"Rix","full_name":"Rix, Hans-Walter","first_name":"Hans-Walter"},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"full_name":"Suess, Katherine A.","first_name":"Katherine A.","last_name":"Suess"},{"first_name":"Bingjie","full_name":"Wang, Bingjie","last_name":"Wang"},{"last_name":"Whitaker","first_name":"Katherine E.","full_name":"Whitaker, Katherine E."},{"full_name":"Williams, Christina C.","first_name":"Christina C.","last_name":"Williams"}],"OA_type":"diamond","article_type":"original","doi":"10.1051/0004-6361/202452186","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 697","date_updated":"2025-09-30T12:45:25Z","oa":1,"publisher":"EDP Sciences","scopus_import":"1","publication":"Astronomy & Astrophysics","volume":697,"type":"journal_article","article_number":"A189","citation":{"ieee":"A. de Graaff et al., “RUBIES: A complete census of the bright and red distant universe with JWST/NIRSpec,” Astronomy & Astrophysics, vol. 697. EDP Sciences, 2025.","apa":"de Graaff, A., Brammer, G., Weibel, A., Lewis, Z., Maseda, M. V., Oesch, P. A., … Williams, C. C. (2025). RUBIES: A complete census of the bright and red distant universe with JWST/NIRSpec. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202452186","chicago":"Graaff, Anna de, Gabriel Brammer, Andrea Weibel, Zach Lewis, Michael V. Maseda, Pascal A. Oesch, Rachel Bezanson, et al. “RUBIES: A Complete Census of the Bright and Red Distant Universe with JWST/NIRSpec.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202452186.","mla":"de Graaff, Anna, et al. “RUBIES: A Complete Census of the Bright and Red Distant Universe with JWST/NIRSpec.” Astronomy & Astrophysics, vol. 697, A189, EDP Sciences, 2025, doi:10.1051/0004-6361/202452186.","ama":"de Graaff A, Brammer G, Weibel A, et al. RUBIES: A complete census of the bright and red distant universe with JWST/NIRSpec. Astronomy & Astrophysics. 2025;697. doi:10.1051/0004-6361/202452186","short":"A. de Graaff, G. Brammer, A. Weibel, Z. Lewis, M.V. Maseda, P.A. Oesch, R. Bezanson, L.A. Boogaard, N.J. Cleri, O.R. Cooper, R. Gottumukkala, J.E. Greene, M. Hirschmann, R.E. Hviding, H. Katz, I. Labbé, J. Leja, J.J. Matthee, I. McConachie, T.B. Miller, R.P. Naidu, S.H. Price, H.-W. Rix, D.J. Setton, K.A. Suess, B. Wang, K.E. Whitaker, C.C. Williams, Astronomy & Astrophysics 697 (2025).","ista":"de Graaff A, Brammer G, Weibel A, Lewis Z, Maseda MV, Oesch PA, Bezanson R, Boogaard LA, Cleri NJ, Cooper OR, Gottumukkala R, Greene JE, Hirschmann M, Hviding RE, Katz H, Labbé I, Leja J, Matthee JJ, McConachie I, Miller TB, Naidu RP, Price SH, Rix H-W, Setton DJ, Suess KA, Wang B, Whitaker KE, Williams CC. 2025. RUBIES: A complete census of the bright and red distant universe with JWST/NIRSpec. Astronomy & Astrophysics. 697, A189."},"article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"external_id":{"isi":["001490583400004"]},"oa_version":"Published Version","acknowledgement":"We thank the CEERS and PRIMER teams for making their imaging data publicly available immediately. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs #1345, #1837 #2234, #2279, #2514, #2750, #3990 and #4233. Support for program #4233 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. REH acknowledges support by the German Aerospace Center (DLR) and the Federal Ministry for Economic Affairs and Energy (BMWi) through program 50OR2403 ‘RUBIES’. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #562. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. Support for this work for RPN was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Open Access funding provided by Max Planck Society.","title":"RUBIES: A complete census of the bright and red distant universe with JWST/NIRSpec","ddc":["520"],"department":[{"_id":"JoMa"}],"date_published":"2025-05-19T00:00:00Z","file":[{"file_size":6874721,"relation":"main_file","date_updated":"2025-06-03T09:25:49Z","content_type":"application/pdf","file_id":"19788","access_level":"open_access","date_created":"2025-06-03T09:25:49Z","success":1,"checksum":"cccf44629f28535dde91f2ebdf38c054","file_name":"2025_AstronomyAstrophysics_deGraaff.pdf","creator":"dernst"}],"date_created":"2025-06-03T08:59:52Z","_id":"19784","has_accepted_license":"1","month":"05","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"year":"2025","quality_controlled":"1","status":"public"},{"oa":1,"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:19791","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"date_updated":"2025-09-30T14:34:42Z","citation":{"chicago":"Desaules, Jean-Yves Marc. “Research Data for ‘Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:19791.","ista":"Desaules J-YM. 2025. Research Data for ‘Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:19791.","short":"J.-Y.M. Desaules, (2025).","mla":"Desaules, Jean-Yves Marc. Research Data for “Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:19791.","ama":"Desaules J-YM. Research Data for “Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory.” 2025. doi:10.15479/AT:ISTA:19791","ieee":"J.-Y. M. Desaules, “Research Data for ‘Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory.’” Institute of Science and Technology Austria, 2025.","apa":"Desaules, J.-Y. M. (2025). Research Data for “Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:19791"},"type":"research_data","day":"04","keyword":["lattice gauge theories","quantum many-body scars","deconfinement"],"abstract":[{"lang":"eng","text":"Confinement is a prominent phenomenon in condensed matter and high-energy physics that has recently become the focus of quantum-simulation experiments of lattice gauge theories (LGTs). As such, a theoretical understanding of the effect of confinement on LGT dynamics is not only of fundamental importance, but can lend itself to upcoming experiments. Here, we show how confinement in a Z2 LGT can be locally avoided by proximity to a resonance between the fermion mass and the electric field strength. Furthermore, we show that this local deconfinement can become global for certain initial conditions, where information transport occurs over the entire chain. In addition, we show how this can lead to strong quantum many-body scarring starting in different initial states. Our findings provide deeper insights into the nature of confinement in Z2 LGTs and can be tested on current and near-term quantum devices."}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:19791","corr_author":"1","file_date_updated":"2025-06-04T14:26:29Z","OA_place":"repository","author":[{"orcid":"0000-0002-3749-6375","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","first_name":"Jean-Yves Marc","full_name":"Desaules, Jean-Yves Marc","last_name":"Desaules"}],"OA_type":"green","has_accepted_license":"1","month":"06","_id":"19791","ec_funded":1,"status":"public","year":"2025","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Preprint","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20327"}],"link":[{"url":"https://arxiv.org/abs/2404.11645","relation":"preprint"}]},"title":"Research Data for \"Mass-Assisted Local Deconfinement in a Confined Z2 Lattice Gauge Theory\"","acknowledgement":"The authors are grateful to Fiona Burnell, Gaurav Gyawali, Zlatko Papi´c, Elliot Rosenberg, Pedram Roushan, and Michael Schecter for insightful discussions. J.-Y.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 101034413. T.I. Acknowledges support from the National Science Foundation under Grant No. DMR-2143635. J.C.H. acknowledges support from the Emmy Noether Programme of the German Research Foundation (DFG) under grant no. HA 8206/1-1.","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-06-04T00:00:00Z","file":[{"file_name":"Data+Code.zip","creator":"jdesaule","date_created":"2025-06-04T14:26:29Z","success":1,"checksum":"a613d73ee05f72a48ae9c97693bdd690","date_updated":"2025-06-04T14:26:29Z","content_type":"application/zip","file_id":"19792","access_level":"open_access","file_size":31946898,"relation":"main_file"},{"access_level":"open_access","content_type":"text/plain","date_updated":"2025-06-04T14:26:29Z","file_id":"19793","file_size":13071,"relation":"other","creator":"jdesaule","file_name":"readme.txt","checksum":"7df1549ce5e2f293d142ecf5e5b89489","date_created":"2025-06-04T14:26:29Z"}],"contributor":[{"last_name":"Desaules","orcid":"0000-0002-3749-6375","contributor_type":"researcher","first_name":"Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80"},{"last_name":"Iadecola","contributor_type":"researcher","first_name":"Thomas"},{"last_name":"Halimeh","contributor_type":"researcher","first_name":"Jad"}],"date_created":"2025-06-04T14:30:22Z","ddc":["530"],"department":[{"_id":"MaSe"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","oa_version":"Published Version","acknowledgement":"The research leading to these results has received support from the National Research Foundation of South Africa, the Deutscher Akademischer Austauschdienst, NOMIS Foundation, NVIDIA Academic Program, the University of Cape Town, the Anna Mueller Grocholski Foundation, the Swiss National Science Foundation (SNSF: 208184), the Gabriel Foundation, a Wellcome Trust Seed Award (214042/Z/18/Z), the South African Medical Research Council and the FLAIR Fellowship Programme (FLR\\R1\\190829): a partnership between the African Academy of Sciences and the Royal Society funded by the UK Government's Global Challenges Research Fund and a Wellcome Trust International Intermediate Fellowship (222968/Z/21/Z).","title":"Network models incorporating chloride dynamics predict optimal strategies for terminating status epilepticus","isi":1,"external_id":{"isi":["001501576500001"]},"department":[{"_id":"TiVo"}],"ddc":["570"],"date_created":"2025-06-08T22:01:22Z","file":[{"file_name":"2025_NeurobioDisease_Currin.pdf","creator":"dernst","success":1,"date_created":"2025-12-30T08:35:41Z","checksum":"abe215be676ed14e9a37fb78b6a5a610","file_id":"20896","date_updated":"2025-12-30T08:35:41Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":7063352}],"date_published":"2025-08-01T00:00:00Z","_id":"19794","publication_identifier":{"issn":["0969-9961"],"eissn":["1095-953X"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"08","year":"2025","status":"public","quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.nbd.2025.106966","OA_place":"publisher","file_date_updated":"2025-12-30T08:35:41Z","corr_author":"1","abstract":[{"text":"Status epilepticus (SE), seizures lasting beyond five minutes, is a medical emergency commonly treated with benzodiazepines which enhance GABAA receptor (GABAAR) conductance. Despite widespread use, benzodiazepines fail in over one-third of patients, potentially due to seizure-induced disruption of neuronal chloride (Cl−) homeostasis. Understanding these changes at a network level is crucial for improving clinical translation. Here, we address this using a large-scale spiking neural network model incorporating Cl− dynamics, informed by clinical EEG and experimental slice recordings. Our simulations confirm that the GABAAR reversal potential (EGABA) dictates the pro- or anti-seizure effect of GABAAR conductance modulation, with high EGABA rendering benzodiazepines ineffective or excitatory. We show SE-like activity and EGABA depend non-linearly on Cl− extrusion efficacy and GABAAR conductance. Critically, cell-type specific manipulations reveal that pyramidal cell, not interneuron, Cl− extrusion predominantly determines the severity of SE activity and the response to simulated benzodiazepines. Leveraging these mechanistic insights, we develop a predictive framework mapping network states to Cl− extrusion capacity and GABAergic load, yielding a proposed decision-making strategy to guide therapeutic interventions based on initial treatment response. This work identifies pyramidal cell Cl− handling as a key therapeutic target and demonstrates the utility of biophysically detailed network models for optimising SE treatment protocols.","lang":"eng"}],"publication_status":"published","day":"01","OA_type":"gold","author":[{"orcid":"0000-0002-4809-5059","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher","full_name":"Currin, Christopher","last_name":"Currin"},{"last_name":"Burman","full_name":"Burman, Richard J.","first_name":"Richard J."},{"last_name":"Fedele","first_name":"Tommaso","full_name":"Fedele, Tommaso"},{"last_name":"Ramantani","first_name":"Georgia","full_name":"Ramantani, Georgia"},{"full_name":"Rosch, Richard E.","first_name":"Richard E.","last_name":"Rosch"},{"last_name":"Sprekeler","full_name":"Sprekeler, Henning","first_name":"Henning"},{"first_name":"Joseph V.","full_name":"Raimondo, Joseph V.","last_name":"Raimondo"}],"article_type":"original","intvolume":" 212","date_updated":"2025-12-30T08:36:36Z","doi":"10.1016/j.nbd.2025.106966","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"scopus_import":"1","publisher":"Elsevier","oa":1,"publication":"Neurobiology of Disease","volume":212,"DOAJ_listed":"1","type":"journal_article","article_number":"106966","citation":{"chicago":"Currin, Christopher, Richard J. Burman, Tommaso Fedele, Georgia Ramantani, Richard E. Rosch, Henning Sprekeler, and Joseph V. Raimondo. “Network Models Incorporating Chloride Dynamics Predict Optimal Strategies for Terminating Status Epilepticus.” Neurobiology of Disease. Elsevier, 2025. https://doi.org/10.1016/j.nbd.2025.106966.","ama":"Currin C, Burman RJ, Fedele T, et al. Network models incorporating chloride dynamics predict optimal strategies for terminating status epilepticus. Neurobiology of Disease. 2025;212. doi:10.1016/j.nbd.2025.106966","mla":"Currin, Christopher, et al. “Network Models Incorporating Chloride Dynamics Predict Optimal Strategies for Terminating Status Epilepticus.” Neurobiology of Disease, vol. 212, 106966, Elsevier, 2025, doi:10.1016/j.nbd.2025.106966.","short":"C. Currin, R.J. Burman, T. Fedele, G. Ramantani, R.E. Rosch, H. Sprekeler, J.V. Raimondo, Neurobiology of Disease 212 (2025).","ista":"Currin C, Burman RJ, Fedele T, Ramantani G, Rosch RE, Sprekeler H, Raimondo JV. 2025. Network models incorporating chloride dynamics predict optimal strategies for terminating status epilepticus. Neurobiology of Disease. 212, 106966.","ieee":"C. Currin et al., “Network models incorporating chloride dynamics predict optimal strategies for terminating status epilepticus,” Neurobiology of Disease, vol. 212. Elsevier, 2025.","apa":"Currin, C., Burman, R. J., Fedele, T., Ramantani, G., Rosch, R. E., Sprekeler, H., & Raimondo, J. V. (2025). Network models incorporating chloride dynamics predict optimal strategies for terminating status epilepticus. Neurobiology of Disease. Elsevier. https://doi.org/10.1016/j.nbd.2025.106966"}},{"has_accepted_license":"1","month":"05","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1367-4811"]},"_id":"19796","ec_funded":1,"year":"2025","status":"public","quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"isi":1,"external_id":{"isi":["001493400600001"],"pmid":["40327535"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/jcrozum/biobalm"}],"record":[{"id":"19800","relation":"research_data","status":"public"}]},"oa_version":"Published Version","title":"Mapping the attractor landscape of Boolean networks with biobalm","acknowledgement":"V.-G.T. was supported by Institut Carnot STAR, Marseille, France. K.H.P. was supported by NSF grant MCB1715826 to Réka Albert. S.P. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. J.C.R. was supported by internal departmental funds provided by Luis M. Rocha. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the article.","article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-05-01T00:00:00Z","file":[{"access_level":"open_access","file_id":"19801","date_updated":"2025-06-10T07:07:45Z","content_type":"application/pdf","file_size":2695801,"relation":"main_file","creator":"dernst","file_name":"2025_Bioinformatics_Trinh.pdf","checksum":"fa9d68aa0f5ce37598a623c9be936f09","success":1,"date_created":"2025-06-10T07:07:45Z"}],"date_created":"2025-06-08T22:01:22Z","ddc":["000"],"department":[{"_id":"ToHe"}],"oa":1,"pmid":1,"publisher":"Oxford University Press","scopus_import":"1","doi":"10.1093/bioinformatics/btaf280","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 41","date_updated":"2025-09-30T12:46:33Z","article_number":"btaf280","citation":{"ieee":"V. G. Trinh, K. H. Park, S. Pastva, and J. C. Rozum, “Mapping the attractor landscape of Boolean networks with biobalm,” Bioinformatics, vol. 41, no. 5. Oxford University Press, 2025.","apa":"Trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. C. (2025). Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaf280","chicago":"Trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan C. Rozum. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics. Oxford University Press, 2025. https://doi.org/10.1093/bioinformatics/btaf280.","ama":"Trinh VG, Park KH, Pastva S, Rozum JC. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 2025;41(5). doi:10.1093/bioinformatics/btaf280","mla":"Trinh, Van Giang, et al. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics, vol. 41, no. 5, btaf280, Oxford University Press, 2025, doi:10.1093/bioinformatics/btaf280.","short":"V.G. Trinh, K.H. Park, S. Pastva, J.C. Rozum, Bioinformatics 41 (2025).","ista":"Trinh VG, Park KH, Pastva S, Rozum JC. 2025. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 41(5), btaf280."},"issue":"5","publication":"Bioinformatics","volume":41,"DOAJ_listed":"1","type":"journal_article","publication_status":"published","day":"01","abstract":[{"text":"Motivation: Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram (SD) describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. Efficient computational tools for studying SDs are essential for the understanding of Boolean attractor landscapes and connecting them to their biological functions.\r\nResults: We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist’s Boolean attractor landscape mapper, biobalm. We compare biobalm to similar tools and find a substantial performance increase in SD construction, attractor identification, and attractor control. We perform the most comprehensive comparative analysis to date of the SD structure in experimentally-validated Boolean models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small SDs, indicating simple decision structures. In contrast, nonrandom models from the literature are enriched in extremely large SDs, indicating an abundance of decision points and suggesting the presence of complex Waddington landscapes in nature.\r\nAvailability and implementation: The tool biobalm is available online at https://github.com/jcrozum/biobalm. Further data, scripts for testing, analysis, and figure generation are available online at https://github.com/jcrozum/biobalm-analysis and in the reproducibility artefact at https://doi.org/10.5281/zenodo.13854760.","lang":"eng"}],"fulldoi":"https://doi.org/10.1093/bioinformatics/btaf280","OA_place":"publisher","corr_author":"1","file_date_updated":"2025-06-10T07:07:45Z","article_type":"original","author":[{"last_name":"Trinh","full_name":"Trinh, Van Giang","first_name":"Van Giang"},{"last_name":"Park","full_name":"Park, Kyu Hyong","first_name":"Kyu Hyong"},{"last_name":"Pastva","first_name":"Samuel","full_name":"Pastva, Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331"},{"last_name":"Rozum","first_name":"Jordan C.","full_name":"Rozum, Jordan C."}],"OA_type":"gold"},{"arxiv":1,"day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"In an n×n array filled with symbols, a transversal is a collection of entries with distinct rows, columns and symbols. In this note we show that if no symbol appears more than βn times, the array contains a transversal of size (1−β/4−o(1))n . In particular, if the array is filled with n symbols, each appearing n times (an equi- n square), we get transversals of size (3/4−o(1))n. Moreover, our proof gives a deterministic algorithm with polynomial running time, that finds these transversals."}],"fulldoi":"https://doi.org/10.1002/jcd.21990","OA_place":"repository","article_type":"original","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"},{"last_name":"Morris","full_name":"Morris, Patrick","first_name":"Patrick"}],"OA_type":"green","oa":1,"scopus_import":"1","publisher":"Wiley","doi":"10.1002/jcd.21990","date_updated":"2025-12-30T08:37:37Z","intvolume":" 33","citation":{"ieee":"M. Anastos and P. Morris, “A note on finding large transversals efficiently,” Journal of Combinatorial Designs, vol. 33, no. 9. Wiley, pp. 338–342, 2025.","apa":"Anastos, M., & Morris, P. (2025). A note on finding large transversals efficiently. Journal of Combinatorial Designs. Wiley. https://doi.org/10.1002/jcd.21990","chicago":"Anastos, Michael, and Patrick Morris. “A Note on Finding Large Transversals Efficiently.” Journal of Combinatorial Designs. Wiley, 2025. https://doi.org/10.1002/jcd.21990.","ama":"Anastos M, Morris P. A note on finding large transversals efficiently. Journal of Combinatorial Designs. 2025;33(9):338-342. doi:10.1002/jcd.21990","mla":"Anastos, Michael, and Patrick Morris. “A Note on Finding Large Transversals Efficiently.” Journal of Combinatorial Designs, vol. 33, no. 9, Wiley, 2025, pp. 338–42, doi:10.1002/jcd.21990.","short":"M. Anastos, P. Morris, Journal of Combinatorial Designs 33 (2025) 338–342.","ista":"Anastos M, Morris P. 2025. A note on finding large transversals efficiently. Journal of Combinatorial Designs. 33(9), 338–342."},"issue":"9","volume":33,"publication":"Journal of Combinatorial Designs","type":"journal_article","isi":1,"external_id":{"isi":["001495472300001"],"arxiv":["2412.05891"]},"oa_version":"Preprint","acknowledgement":"We are very grateful to Matthew Kwan and Alp Müyesser with whom we had many interesting discussions leading to the results of this note. We also thank the anonymous reviewers for their suggestions improving the presentation of this note.\r\n\r\nMA was supported by the Austrian Science Fund (FWF) [10.55776/ESP3863424] and by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant—project number 101034413. PM was supported by the European Union's Horizon Europe Marie Skłodowska-Curie grant RAND-COMB-DESIGN—project number 101106032.","title":"A note on finding large transversals efficiently","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-09-01T00:00:00Z","date_created":"2025-06-08T22:01:23Z","department":[{"_id":"MaKw"}],"month":"09","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1063-8539"],"eissn":["1520-6610"]},"_id":"19798","ec_funded":1,"status":"public","quality_controlled":"1","year":"2025","project":[{"name":"Combinatorial Optimisation Problems on Sparse Random Graphs","_id":"8f906bd2-16d5-11f0-9cad-e07be8aa9ac9","grant_number":"ESP3863424"},{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.05891","open_access":"1"}],"page":"338-342"},{"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","quality_controlled":"1","year":"2025","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"06","has_accepted_license":"1","ec_funded":1,"_id":"19833","date_created":"2025-06-13T06:09:38Z","file":[{"file_name":"2025_PhysReviewB_Brighi.pdf","creator":"dernst","success":1,"date_created":"2025-06-23T06:28:17Z","checksum":"7941f92124793a383ca132eee2c289c5","file_id":"19861","content_type":"application/pdf","date_updated":"2025-06-23T06:28:17Z","access_level":"open_access","file_size":1082749,"relation":"main_file"}],"date_published":"2025-06-12T00:00:00Z","department":[{"_id":"MaSe"}],"ddc":["530"],"acknowledgement":"We thank D. A. Abanin for insightful discussions in the early stages of this work. P.B. acknowledges support by the Austrian Science Fund (FWF) [Grant Agreement No. 10.55776/ESP9057324]. This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1]. The authors acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy–EXC-2111–390814868. The authors acknowledge PRACE for awarding access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [52].","title":"Probing the many-body localized spin-glass phase through quench dynamics","oa_version":"Published Version","external_id":{"isi":["001511503800006"],"arxiv":["2502.08192"]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (in subscription journal)","citation":{"ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Probing the many-body localized spin-glass phase through quench dynamics,” Physical Review B, vol. 111, no. 22. American Physical Society, 2025.","apa":"Brighi, P., Ljubotina, M., & Serbyn, M. (2025). Probing the many-body localized spin-glass phase through quench dynamics. Physical Review B. American Physical Society. https://doi.org/10.1103/9fms-ygfz","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Probing the Many-Body Localized Spin-Glass Phase through Quench Dynamics.” Physical Review B. American Physical Society, 2025. https://doi.org/10.1103/9fms-ygfz.","ista":"Brighi P, Ljubotina M, Serbyn M. 2025. Probing the many-body localized spin-glass phase through quench dynamics. Physical Review B. 111(22), L220202.","short":"P. Brighi, M. Ljubotina, M. Serbyn, Physical Review B 111 (2025).","mla":"Brighi, Pietro, et al. “Probing the Many-Body Localized Spin-Glass Phase through Quench Dynamics.” Physical Review B, vol. 111, no. 22, L220202, American Physical Society, 2025, doi:10.1103/9fms-ygfz.","ama":"Brighi P, Ljubotina M, Serbyn M. Probing the many-body localized spin-glass phase through quench dynamics. Physical Review B. 2025;111(22). doi:10.1103/9fms-ygfz"},"article_number":"L220202","type":"journal_article","publication":"Physical Review B","volume":111,"issue":"22","scopus_import":"1","publisher":"American Physical Society","oa":1,"date_updated":"2025-09-30T12:48:10Z","intvolume":" 111","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1103/9fms-ygfz","article_type":"letter_note","OA_type":"hybrid","author":[{"last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729"},{"last_name":"Ljubotina","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"publication_status":"published","day":"12","arxiv":1,"OA_place":"publisher","file_date_updated":"2025-06-23T06:28:17Z","fulldoi":"https://doi.org/10.1103/9fms-ygfz","abstract":[{"lang":"eng","text":"Eigenstates of quantum many-body systems are often used to define phases of matter in and out of equilibrium; however, experimentally accessing highly excited eigenstates is a challenging task, calling for alternative strategies to dynamically probe nonequilibrium phases. In this work, we characterize the dynamical properties of a disordered spin chain, focusing on the spin-glass regime. Using tensor-network simulations, we observe oscillatory behavior of local expectation values and bipartite entanglement entropy. We explain these oscillations deep in the many-body localized spin-glass regime via a simple theoretical model. From perturbation theory, we predict the timescales up to which our analytical description is valid and confirm it with numerical simulations. Finally, we study the correlation length dynamics, which, after a long-time plateau, resume growing in line with renormalization group (RG) expectations. Our work suggests that RG predictions can be quantitatively tested against numerical simulations and experiments, potentially enabling microscopic descriptions of dynamical phases in large systems."}]},{"doi":"10.1038/s43247-025-02379-x","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 6","date_updated":"2025-09-30T12:48:43Z","oa":1,"pmid":1,"publisher":"Springer Nature","scopus_import":"1","publication":"Communications Earth and Environment","volume":6,"type":"journal_article","article_number":"434","citation":{"ama":"Fyffe CL, Potter E, Miles E, et al. Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes. Communications Earth and Environment. 2025;6. doi:10.1038/s43247-025-02379-x","mla":"Fyffe, Catriona Louise, et al. “Thin and Ephemeral Snow Shapes Melt and Runoff Dynamics in the Peruvian Andes.” Communications Earth and Environment, vol. 6, 434, Springer Nature, 2025, doi:10.1038/s43247-025-02379-x.","short":"C.L. Fyffe, E. Potter, E. Miles, T. Shaw, M. McCarthy, A. Orr, E. Loarte, K. Medina, S. Fatichi, R. Hellström, M. Baraer, E. Mateo, A. Cochachin, M. Westoby, F. Pellicciotti, Communications Earth and Environment 6 (2025).","ista":"Fyffe CL, Potter E, Miles E, Shaw T, McCarthy M, Orr A, Loarte E, Medina K, Fatichi S, Hellström R, Baraer M, Mateo E, Cochachin A, Westoby M, Pellicciotti F. 2025. Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes. Communications Earth and Environment. 6, 434.","chicago":"Fyffe, Catriona Louise, Emily Potter, Evan Miles, Thomas Shaw, Michael McCarthy, Andrew Orr, Edwin Loarte, et al. “Thin and Ephemeral Snow Shapes Melt and Runoff Dynamics in the Peruvian Andes.” Communications Earth and Environment. Springer Nature, 2025. https://doi.org/10.1038/s43247-025-02379-x.","apa":"Fyffe, C. L., Potter, E., Miles, E., Shaw, T., McCarthy, M., Orr, A., … Pellicciotti, F. (2025). Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes. Communications Earth and Environment. Springer Nature. https://doi.org/10.1038/s43247-025-02379-x","ieee":"C. L. Fyffe et al., “Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes,” Communications Earth and Environment, vol. 6. Springer Nature, 2025."},"abstract":[{"lang":"eng","text":"The snow and glaciers of the Peruvian Andes provide vital water supplies in a region facing water scarcity and substantial glacier change. However, there remains a lack of understanding of snow processes and quantification of the contribution of melt to runoff. Here we apply a distributed glacio-hydrological model over the Rio Santa basin to disentangle the role of the cryosphere in the Andean water cycle. Only at the highest elevations (>5000 m a.s.l.) is the snow cover continuous; at lower elevations, the snowpack is thin and ephemeral, with rapid cycles of snowfall and melt. Due to the large catchment area affected by ephemeral snow, its contribution to catchment inputs is substantial (23% and 38% in the wet and dry season, respectively). Ice melt is crucial in the mid-dry season (up to 44% of inputs). Our results improve estimates of water fluxes and call for further process-based modelling across the Andes."}],"fulldoi":"https://doi.org/10.1038/s43247-025-02379-x","corr_author":"1","OA_place":"publisher","file_date_updated":"2025-06-23T06:41:15Z","publication_status":"published","day":"05","author":[{"last_name":"Fyffe","id":"001b0422-8d15-11ed-bc51-cab6c037a228","first_name":"Catriona Louise","full_name":"Fyffe, Catriona Louise"},{"last_name":"Potter","first_name":"Emily","full_name":"Potter, Emily"},{"first_name":"Evan","full_name":"Miles, Evan","last_name":"Miles"},{"last_name":"Shaw","orcid":"0000-0001-7640-6152","first_name":"Thomas","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e"},{"last_name":"Mccarthy","full_name":"Mccarthy, Michael","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f"},{"full_name":"Orr, Andrew","first_name":"Andrew","last_name":"Orr"},{"first_name":"Edwin","full_name":"Loarte, Edwin","last_name":"Loarte"},{"full_name":"Medina, Katy","first_name":"Katy","last_name":"Medina"},{"last_name":"Fatichi","full_name":"Fatichi, Simone","first_name":"Simone"},{"last_name":"Hellström","full_name":"Hellström, Rob","first_name":"Rob"},{"full_name":"Baraer, Michel","first_name":"Michel","last_name":"Baraer"},{"last_name":"Mateo","full_name":"Mateo, Emilio","first_name":"Emilio"},{"full_name":"Cochachin, Alejo","first_name":"Alejo","last_name":"Cochachin"},{"last_name":"Westoby","first_name":"Matthew","full_name":"Westoby, Matthew"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","orcid":"0000-0002-5554-8087"}],"OA_type":"gold","article_type":"original","_id":"19839","has_accepted_license":"1","month":"06","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2662-4435"]},"year":"2025","status":"public","quality_controlled":"1","project":[{"name":"ExPloring the ecohydrological Impacts of a changing Cryosphere in the Peruvian Andes","_id":"bdbe6627-d553-11ed-ba76-b5c9eedf278f","grant_number":"101105480"}],"article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"external_id":{"isi":["001503932400002"],"pmid":["40486185"]},"oa_version":"Published Version","title":"Thin and ephemeral snow shapes melt and runoff dynamics in the Peruvian Andes","acknowledgement":"This work was conducted under the PeruGROWS and PEGASUS projects, which were both funded by NERC (grants NE/S013296/1 and NE/S013318/1, respectively) and CONCYTEC through the Newton-Paulet Fund. The Peruvian part of the Peru GROWS project was conducted within the framework of the call E031-2018-01-NERC Glacier Research Circles through its executing unit FONDECYT (Contract N°08-2019-FONDECYT). Francesca Pellicciotti acknowledges support from the SNSF-funded PASTURE project, grant no. 202604. Catriona Fyffe was supported by the Marie Skłodowska-Curie Action project EPIC, which was funded by the European Union (grant number 101105480). We thank Florian von Ah for calculating the altitudinally resolved glacier mass balances for the catchment. We also thank Duncan Quincey for his support and guidance within both the PeruGROWS and PEGASUS projects. Gerardo Jacome and Alan Llacza are thanked for their contribution to the climate modelling. We thank Ignacio López-Moreno and Simon Gascoin for their thoughtful and constructive comments, which greatly improved the manuscript. The team dedicates this work to the memory of Ing. Alejo Cochachin Rapre, and his tireless work to monitor the region’s glaciers.","ddc":["550"],"department":[{"_id":"FrPe"}],"date_published":"2025-06-05T00:00:00Z","date_created":"2025-06-15T22:01:28Z","file":[{"date_created":"2025-06-23T06:41:15Z","success":1,"checksum":"5d5317640abe280c4f4edfca732cf4e0","file_name":"2025_CommEarthEnvir_Fyffe.pdf","creator":"dernst","file_size":3172494,"relation":"main_file","content_type":"application/pdf","date_updated":"2025-06-23T06:41:15Z","file_id":"19862","access_level":"open_access"}]},{"department":[{"_id":"IlCa"}],"ddc":["520"],"date_created":"2025-06-15T22:01:29Z","file":[{"creator":"dernst","file_name":"2025_MonthlyNoticesRAS_Cunningham.pdf","checksum":"5e675d3696c222e919d6916bad194b01","success":1,"date_created":"2025-06-23T07:28:36Z","access_level":"open_access","file_id":"19864","content_type":"application/pdf","date_updated":"2025-06-23T07:28:36Z","relation":"main_file","file_size":3212636}],"date_published":"2025-06-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","oa_version":"Published Version","acknowledgement":"We thank Matthias Schreiber for his insightful comments. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51527.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. Support for this work was provided by NASA through Chandra Award Number GO4-25014X issued by the Chandra X-ray Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS8-03060. IC was also supported by NASA through grants from the Space Telescope Science Institute, under NASA contracts NASA.22K1813, NAS5-26555, and NAS5-03127. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 101020057). This research was supported in part by grant NSF PHY-1748958 to the Kavli Institute for Theoretical Physics (KITP). PJW acknowledges support from the UK Science and Technology Facilities Council (STFC) through consolidated grants ST/T000406/1 and ST/X001121/1. RA was supported by NASA through the NASA Hubble Fellowship grant #HST-HF2-51499.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555.\r\n\r\nThis research has made use of data obtained from the 4XMM XMM–Newton Serendipitous Source Catalogue compiled by the 10 institutes of the XMM–Newton Survey Science Centre selected by ESA. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. The Pan-STARRS1 Surveys (PS1) and the PS1 public science archive have been made possible through contributions by the Institute for Astronomy, the University of Hawaii, the Pan-STARRS Project Office, the Max-Planck Society and its participating institutes, the Max Planck Institute for Astronomy, Heidelberg and the Max Planck Institute for Extraterrestrial Physics, Garching, The Johns Hopkins University, Durham University, the University of Edinburgh, the Queen’s University Belfast, the Harvard–Smithsonian Center for Astrophysics, the Las Cumbres Observatory Global Telescope Network Incorporated, the National Central University of Taiwan, the Space Telescope Science Institute, the National Aeronautics and Space Administration under grant no. NNX08AR22G issued through the Planetary Science Division of the NASA Science Mission Directorate, the National Science Foundation grant no. AST–1238877, the University of Maryland, Eotvos Lorand University (ELTE), the Los Alamos National Laboratory, and the Gordon and Betty Moore Foundation. This work is based in part on data obtained as part of the UKIDSS. This research made use of hips2fits,4 a service provided by CDS, and of astropy (Astropy Collaboration 2013).","title":"Discovery of two new polars evolved past the period bounce","isi":1,"external_id":{"arxiv":["2503.12675"],"isi":["001493143700001"]},"page":"633-649","year":"2025","quality_controlled":"1","status":"public","_id":"19840","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"06","OA_type":"gold","author":[{"last_name":"Cunningham","first_name":"Tim","full_name":"Cunningham, Tim"},{"last_name":"Caiazzo","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","full_name":"Caiazzo, Ilaria","first_name":"Ilaria","orcid":"0000-0002-4770-5388"},{"first_name":"Gracjan","full_name":"Sienkiewicz, Gracjan","last_name":"Sienkiewicz"},{"last_name":"Wheatley","full_name":"Wheatley, Peter J.","first_name":"Peter J."},{"full_name":"Gänsicke, Boris T.","first_name":"Boris T.","last_name":"Gänsicke"},{"last_name":"El-Badry","full_name":"El-Badry, Kareem","first_name":"Kareem"},{"last_name":"Arcodia","first_name":"Riccardo","full_name":"Arcodia, Riccardo"},{"first_name":"David","full_name":"Charbonneau, David","last_name":"Charbonneau"},{"last_name":"Connor","first_name":"Liam","full_name":"Connor, Liam"},{"full_name":"De, Kishalay","first_name":"Kishalay","last_name":"De"},{"full_name":"Hakala, Pasi","first_name":"Pasi","last_name":"Hakala"},{"full_name":"Kenyon, Scott J.","first_name":"Scott J.","last_name":"Kenyon"},{"full_name":"Maheshwari, Sumit Kumar","first_name":"Sumit Kumar","last_name":"Maheshwari"},{"last_name":"Rodriguez","full_name":"Rodriguez, Antonio C.","first_name":"Antonio C."},{"full_name":"Van Roestel, Jan","first_name":"Jan","last_name":"Van Roestel"},{"last_name":"Tremblay","full_name":"Tremblay, Pier Emmanuel","first_name":"Pier Emmanuel"}],"article_type":"original","fulldoi":"https://doi.org/10.1093/mnras/staf561","file_date_updated":"2025-06-23T07:28:36Z","OA_place":"publisher","abstract":[{"text":"We report the discovery of two new magnetic cataclysmic variables with brown dwarf companions and long orbital periods (P_{\\rm orb}=95\\pm1 and 104\\pm2 min). This discovery increases the sample of candidate magnetic period bouncers with confirmed sub-stellar donors from four to six. We also find their X-ray luminosity from archival XMM–Newton observations to be in the range L_{\\rm X}\\approx10^{28}-10^{29} \\mathrm{erg\\,s^{-1}} in the 0.25–10 keV band. This low luminosity is comparable with the other candidates, and at least an order of magnitude lower than the X-ray luminosities typically measured in cataclysmic variables. The X-ray fluxes imply mass transfer rates that are much lower than predicted by evolutionary models, even if some of the discrepancy is due to the accretion energy being emitted in other bands, such as via cyclotron emission at infrared wavelengths. Although it is possible that some or all of these systems formed directly as binaries containing a brown dwarf, it is likely that the donor used to be a low-mass star and that the systems followed the evolutionary track for cataclysmic variables, evolving past the period bounce. The donor in long period systems is expected to be a low-mass, cold brown dwarf. This hypothesis is supported by near-infrared photometric observations that constrain the donors in the two systems to be brown dwarfs cooler than \r\n1100 K (spectral types T5 or later), most likely losing mass via Roche Lobe overflow or winds. The serendipitous discovery of two magnetic period bouncers in the small footprint of the XMM–Newton catalogue implies a large space density of these type of systems, possibly compatible with the prediction of 40–70 per cent of magnetic cataclysmic variables to be period bouncers.","lang":"eng"}],"day":"01","publication_status":"published","arxiv":1,"volume":540,"publication":"Monthly Notices of the Royal Astronomical Society","type":"journal_article","issue":"1","citation":{"apa":"Cunningham, T., Caiazzo, I., Sienkiewicz, G., Wheatley, P. J., Gänsicke, B. T., El-Badry, K., … Tremblay, P. E. (2025). Discovery of two new polars evolved past the period bounce. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staf561","ieee":"T. Cunningham et al., “Discovery of two new polars evolved past the period bounce,” Monthly Notices of the Royal Astronomical Society, vol. 540, no. 1. Oxford University Press, pp. 633–649, 2025.","ama":"Cunningham T, Caiazzo I, Sienkiewicz G, et al. Discovery of two new polars evolved past the period bounce. Monthly Notices of the Royal Astronomical Society. 2025;540(1):633-649. doi:10.1093/mnras/staf561","mla":"Cunningham, Tim, et al. “Discovery of Two New Polars Evolved Past the Period Bounce.” Monthly Notices of the Royal Astronomical Society, vol. 540, no. 1, Oxford University Press, 2025, pp. 633–49, doi:10.1093/mnras/staf561.","short":"T. Cunningham, I. Caiazzo, G. Sienkiewicz, P.J. Wheatley, B.T. Gänsicke, K. El-Badry, R. Arcodia, D. Charbonneau, L. Connor, K. De, P. Hakala, S.J. Kenyon, S.K. Maheshwari, A.C. Rodriguez, J. Van Roestel, P.E. Tremblay, Monthly Notices of the Royal Astronomical Society 540 (2025) 633–649.","ista":"Cunningham T, Caiazzo I, Sienkiewicz G, Wheatley PJ, Gänsicke BT, El-Badry K, Arcodia R, Charbonneau D, Connor L, De K, Hakala P, Kenyon SJ, Maheshwari SK, Rodriguez AC, Van Roestel J, Tremblay PE. 2025. Discovery of two new polars evolved past the period bounce. Monthly Notices of the Royal Astronomical Society. 540(1), 633–649.","chicago":"Cunningham, Tim, Ilaria Caiazzo, Gracjan Sienkiewicz, Peter J. Wheatley, Boris T. Gänsicke, Kareem El-Badry, Riccardo Arcodia, et al. “Discovery of Two New Polars Evolved Past the Period Bounce.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2025. https://doi.org/10.1093/mnras/staf561."},"intvolume":" 540","date_updated":"2025-09-30T12:50:33Z","doi":"10.1093/mnras/staf561","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"Oxford University Press","scopus_import":"1","oa":1},{"article_number":"A57","citation":{"chicago":"Östlin, Göran, Pablo G. Pérez-González, Jens Melinder, Steven Gillman, Edoardo Iani, Luca Costantin, Leindert A. Boogaard, et al. “MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey Description and Early Results for the Galaxy Population Detected at 5.6 Μm.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202451723.","mla":"Östlin, Göran, et al. “MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey Description and Early Results for the Galaxy Population Detected at 5.6 Μm.” Astronomy & Astrophysics, vol. 696, A57, EDP Sciences, 2025, doi:10.1051/0004-6361/202451723.","ama":"Östlin G, Pérez-González PG, Melinder J, et al. MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey description and early results for the galaxy population detected at 5.6 µm. Astronomy & Astrophysics. 2025;696. doi:10.1051/0004-6361/202451723","ista":"Östlin G, Pérez-González PG, Melinder J, Gillman S, Iani E, Costantin L, Boogaard LA, Rinaldi P, Colina L, Nørgaard-Nielsen HU, Dicken D, Greve TR, Wright G, Alonso-Herrero A, Álvarez-Márquez J, Annunziatella M, Bik A, Bosman SEI, Caputi KI, Gomez AC, Eckart A, Garcia-Marin M, Hjorth J, Ilbert O, Jermann I, Kendrew S, Labiano A, Langeroodi D, Le Fevre O, Libralato M, Meyer RA, Moutard T, Peissker F, Pye JP, Tikkanen TV, Topinka M, Walter F, Ward M, Van Der Werf P, Van Dishoeck EF, Güdel M, Henning T, Lagage PO, Ray TP, Vandenbussche B. 2025. MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey description and early results for the galaxy population detected at 5.6 µm. Astronomy & Astrophysics. 696, A57.","short":"G. Östlin, P.G. Pérez-González, J. Melinder, S. Gillman, E. Iani, L. Costantin, L.A. Boogaard, P. Rinaldi, L. Colina, H.U. Nørgaard-Nielsen, D. Dicken, T.R. Greve, G. Wright, A. Alonso-Herrero, J. Álvarez-Márquez, M. Annunziatella, A. Bik, S.E.I. Bosman, K.I. Caputi, A.C. Gomez, A. Eckart, M. Garcia-Marin, J. Hjorth, O. Ilbert, I. Jermann, S. Kendrew, A. Labiano, D. Langeroodi, O. Le Fevre, M. Libralato, R.A. Meyer, T. Moutard, F. Peissker, J.P. Pye, T.V. Tikkanen, M. Topinka, F. Walter, M. Ward, P. Van Der Werf, E.F. Van Dishoeck, M. Güdel, T. Henning, P.O. Lagage, T.P. Ray, B. Vandenbussche, Astronomy & Astrophysics 696 (2025).","ieee":"G. Östlin et al., “MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey description and early results for the galaxy population detected at 5.6 µm,” Astronomy & Astrophysics, vol. 696. EDP Sciences, 2025.","apa":"Östlin, G., Pérez-González, P. G., Melinder, J., Gillman, S., Iani, E., Costantin, L., … Vandenbussche, B. (2025). MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey description and early results for the galaxy population detected at 5.6 µm. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202451723"},"volume":696,"publication":"Astronomy & Astrophysics","type":"journal_article","publisher":"EDP Sciences","scopus_import":"1","oa":1,"date_updated":"2026-02-16T12:10:36Z","intvolume":" 696","doi":"10.1051/0004-6361/202451723","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","OA_type":"diamond","author":[{"full_name":"Östlin, Göran","first_name":"Göran","last_name":"Östlin"},{"first_name":"Pablo G.","full_name":"Pérez-González, Pablo G.","last_name":"Pérez-González"},{"last_name":"Melinder","full_name":"Melinder, Jens","first_name":"Jens"},{"last_name":"Gillman","full_name":"Gillman, Steven","first_name":"Steven"},{"orcid":"0000-0001-8386-3546","id":"4053390a-6b68-11ef-9828-a3b8adef8d0a","first_name":"Edoardo","full_name":"Iani, Edoardo","last_name":"Iani"},{"first_name":"Luca","full_name":"Costantin, Luca","last_name":"Costantin"},{"full_name":"Boogaard, Leindert A.","first_name":"Leindert A.","last_name":"Boogaard"},{"first_name":"Pierluigi","full_name":"Rinaldi, Pierluigi","last_name":"Rinaldi"},{"full_name":"Colina, Luis","first_name":"Luis","last_name":"Colina"},{"last_name":"Nørgaard-Nielsen","first_name":"Hans Ulrik","full_name":"Nørgaard-Nielsen, Hans Ulrik"},{"first_name":"Daniel","full_name":"Dicken, Daniel","last_name":"Dicken"},{"last_name":"Greve","full_name":"Greve, Thomas R.","first_name":"Thomas R."},{"last_name":"Wright","first_name":"Gillian","full_name":"Wright, Gillian"},{"first_name":"Almudena","full_name":"Alonso-Herrero, Almudena","last_name":"Alonso-Herrero"},{"last_name":"Álvarez-Márquez","full_name":"Álvarez-Márquez, Javier","first_name":"Javier"},{"last_name":"Annunziatella","full_name":"Annunziatella, Marianna","first_name":"Marianna"},{"full_name":"Bik, Arjan","first_name":"Arjan","last_name":"Bik"},{"last_name":"Bosman","full_name":"Bosman, Sarah E.I.","first_name":"Sarah E.I."},{"last_name":"Caputi","first_name":"Karina I.","full_name":"Caputi, Karina I."},{"last_name":"Gomez","full_name":"Gomez, Alejandro Crespo","first_name":"Alejandro Crespo"},{"first_name":"Andreas","full_name":"Eckart, Andreas","last_name":"Eckart"},{"full_name":"Garcia-Marin, Macarena","first_name":"Macarena","last_name":"Garcia-Marin"},{"last_name":"Hjorth","full_name":"Hjorth, Jens","first_name":"Jens"},{"full_name":"Ilbert, Olivier","first_name":"Olivier","last_name":"Ilbert"},{"full_name":"Jermann, Iris","first_name":"Iris","last_name":"Jermann"},{"last_name":"Kendrew","full_name":"Kendrew, Sarah","first_name":"Sarah"},{"last_name":"Labiano","first_name":"Alvaro","full_name":"Labiano, Alvaro"},{"last_name":"Langeroodi","full_name":"Langeroodi, Danial","first_name":"Danial"},{"full_name":"Le Fevre, Olivier","first_name":"Olivier","last_name":"Le Fevre"},{"last_name":"Libralato","full_name":"Libralato, Mattia","first_name":"Mattia"},{"full_name":"Meyer, Romain A.","first_name":"Romain A.","last_name":"Meyer"},{"full_name":"Moutard, Thibaud","first_name":"Thibaud","last_name":"Moutard"},{"last_name":"Peissker","first_name":"Florian","full_name":"Peissker, Florian"},{"first_name":"John P.","full_name":"Pye, John P.","last_name":"Pye"},{"last_name":"Tikkanen","full_name":"Tikkanen, Tuomo V.","first_name":"Tuomo V."},{"last_name":"Topinka","full_name":"Topinka, Martin","first_name":"Martin"},{"last_name":"Walter","full_name":"Walter, Fabian","first_name":"Fabian"},{"full_name":"Ward, Martin","first_name":"Martin","last_name":"Ward"},{"first_name":"Paul","full_name":"Van Der Werf, Paul","last_name":"Van Der Werf"},{"last_name":"Van Dishoeck","full_name":"Van Dishoeck, Ewine F.","first_name":"Ewine F."},{"last_name":"Güdel","full_name":"Güdel, Manuel","first_name":"Manuel"},{"last_name":"Henning","first_name":"Thomas","full_name":"Henning, Thomas"},{"last_name":"Lagage","full_name":"Lagage, Pierre Olivier","first_name":"Pierre Olivier"},{"full_name":"Ray, Tom P.","first_name":"Tom P.","last_name":"Ray"},{"full_name":"Vandenbussche, Bart","first_name":"Bart","last_name":"Vandenbussche"}],"publication_status":"published","arxiv":1,"day":"01","fulldoi":"https://doi.org/10.1051/0004-6361/202451723","OA_place":"publisher","file_date_updated":"2025-06-23T07:46:01Z","abstract":[{"text":"Context. The recently launched James Webb Space Telescope (JWST) is opening new observing windows on the distant Universe. Among JWST’s instruments, the Mid Infrared Instrument (MIRI) offers the unique capability of imaging observations at wavelengths of λ > 5 μm. This enables unique access to the rest frame near-infrared (NIR, λ ≥ 1 μm) emission from galaxies at redshifts of z > 4 and the visual (λ ≳ 5000 Å) rest frame for z > 9. We report here on the guaranteed time observations (GTO), from the MIRI European Consortium, of the Hubble Ultra Deep Field (HUDF), forming the MIRI Deep Imaging Survey (MIDIS), consisting of an on source integration time of ∼41 hours in the MIRI/F560W (5.6 μm) filter. The F560W filter was selected since it would produce the deepest data in terms of AB magnitudes in a given time. To our knowledge, this constitutes the longest single filter exposure obtained with JWST of an extragalactic field as of yet.\r\nAims. The HUDF is one of the most observed extragalactic fields, with extensive multi-wavelength coverage, where (before JWST) galaxies up to z ∼ 7 have been confirmed, and at z > 10 suggested, from HST photometry. We aim to characterise the galaxy population in HUDF at 5.6 μm, enabling studies such as: the rest frame NIR morphologies for galaxies at z ≲ 4.6, probing mature stellar populations and emission lines in z > 6 sources, intrinsically red and dusty galaxies, and active galactic nuclei (AGNs) and their host galaxies at intermediate redshifts.\r\n\r\nMethods. We reduced the MIRI data using the official JWST pipeline, augmented by in-house custom scripts. We measured the noise characteristics of the resulting image. Galaxy photometry was obtained, and photometric redshifts were estimated for sources with available multi-wavelength photometry (and compared to spectroscopic redshifts when available).\r\n\r\nResults. Over the deepest part of our image, the 5σ point source limit is 28.65 mag AB (12.6 nJy), ∼0.35 mag better than predicted by the JWST exposure time calculator. We find ∼2500 sources, the overwhelming majority of which are distant galaxies, but we note that spurious sources likely remain at faint magnitudes due to imperfect cosmic ray rejection in the JWST pipeline. More than 500 galaxies with available spectroscopic redshifts, up to z ≈ 11, have been identified, the majority of which are at z < 6. More than 1000 galaxies have reliable photometric redshift estimates, of which ∼25 are at 6 < z < 12. The point spread function in the F560W filter has a full width at half maximum (FWHM) of ≈0.2″ (corresponding to 1.4 kpc at z = 4), allowing the NIR rest frame morphologies and stellar mass distributions to be resolved for z < 4.5. Moreover, > 100 objects with very red NIRCam vs MIRI (3.6–5.6 μm > 1 mag) colours have been found, suggestive of dusty or old stellar populations at high redshifts.\r\n\r\nConclusions. We conclude that MIDIS surpasses preflight expectations and that deep MIRI imaging has great potential to characterise the galaxy population from cosmic noon to dawn.","lang":"eng"}],"quality_controlled":"1","status":"public","year":"2025","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"04","_id":"19845","file":[{"file_name":"2025_AstronomyAstrophysics_Oestlin.pdf","creator":"dernst","success":1,"date_created":"2025-06-23T07:46:01Z","checksum":"67600eba8bda24987a130ac334f10456","file_id":"19865","content_type":"application/pdf","date_updated":"2025-06-23T07:46:01Z","access_level":"open_access","relation":"main_file","file_size":15858045}],"date_created":"2025-06-15T22:01:30Z","date_published":"2025-04-01T00:00:00Z","department":[{"_id":"JoMa"}],"ddc":["520"],"oa_version":"Published Version","acknowledgement":"We dedicate this paper to the memory of our deceased and much valued MIRI-EC team members Hans Ulrik Nørgaard-Nielsen and Olivier Le Fèvre, both of whom played a central role in defining the MIDIS project. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The work presented is the effort of the entire MIRI team and the enthusiasm within the MIRI partnership is a significant factor in its success. The following National and International Funding Agencies funded and supported the MIRI development: NASA; ESA; Belgian Science Policy Office (BELSPO); Centre Nationale d’Etudes Spatiales (CNES); Danish National Space Centre; Deutsches Zentrum fur Luftund Raumfahrt (DLR); Enterprise Ireland; Ministerio De Economia y Competividad; Netherlands Research School for Astronomy (NOVA); Netherlands Organisation for Scientific Research (NWO); Science and Technology Facilities Council; Swiss Space Office; Swedish National Space Agency (SNSA); and UK Space Agency. MIRI drew on the scientific and technical expertise of the following organizations: Ames Research Center, USA; Airbus Defence and Space, UK; CEAIrfu, Saclay, France; Centre Spatial de Liège, Belgium; Consejo Superior de Investigaciones Cientficas, Spain; Carl Zeiss Optronics, Germany; Chalmers University of Technology, Sweden; Danish Space Research Institute, Denmark; Dublin Institute for Advanced Studies, Ireland; European Space Agency, Netherlands; ETCA, Belgium; ETH Zurich, Switzerland; Goddard Space Flight Center, USA; Institute d’Astrophysique Spatiale, France; Instituto Nacional de Técnica Aeroespacial,Spain; Institute for Astronomy, Edinburgh, UK; Jet Propulsion Laboratory, USA; Laboratoire d’Astrophysique de Marseille (LAM), France; Leiden University, Netherlands; Lockheed Advanced Technology Center (USA); NOVA Opt-IR group at Dwingeloo, Netherlands; Northrop Grumman, USA; Max Planck Institut f ür Astronomie (MPIA), Heidelberg, Germany; Laboratoire d’Etudes Spatiales et d’Instrumentation en Astrophysique (LESIA), France; Paul Scherrer Institut, Switzerland; Raytheon Vision Systems, USA; RUAG Aerospace, Switzerland; Rutherford Appleton Laboratory (RAL Space), UK; Space Telescope Science Institute, USA; Stockholm University, Sweden; Toegepast- Natuurwetenschappelijk Onderzoek (TNOTPD), Netherlands; UK Astronomy Technology Centre, UK; University College London, UK; University of Amsterdam, Netherlands; University of Arizona, USA; University of Cardiff, UK; University of Cologne, Germany; University of Ghent; University of Groningen, Netherlands; University of Leicester, UK; University of Leuven, Belgium; Utah State University, USA. Additional acknowledgements related to specific grants: G.Ö., J.M. and A.B. acknowledges funding from the Swedish National Space Administration (SNSA). P.G.P.-G. acknowledges support from grant PID2022-139567NB-I00 funded by Spanish Ministerio de Ciencia e Innovación MCIN/AEI/10.13039/501100011033, FEDER Una manera de hacer Europa. This work was supported by research grants (VIL16599,VIL54489) from VILLUM FONDEN. L.C. and J.A.-M. acknowledge support by grant PIB2021-127718NB-100 from the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. M.A. acknowledges financial support from Comunidad de Madrid under Atracción de Talento grant 2020-T2/TIC-19971. J.P.P. and T.V.T. acknowledge financial support from the UK Science and Technology Facilities Council, and the UK Space Agency. A.A.-H. acknowledges financial support from grant PID2021-124665NB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. E.I. and K.I.C. acknowledge funding from the Netherlands Research School for Astronomy (NOVA). K.I.C. acknowledges funding from the Dutch Research Council (NWO) through the award of the Vici Grant VI.C.212.036. RAM acknowledges support from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The paper uses JWST data from programme #1283, obtained from the Barbara Mikulski Archive for Space Telescopes at the Space Telescope Science Institute (STScI). For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) licence to the Author Accepted Manuscript version arising from this submission.","title":"MIRI Deep Imaging Survey (MIDIS) of the Hubble Ultra Deep Field: Survey description and early results for the galaxy population detected at 5.6 µm","isi":1,"external_id":{"arxiv":["2411.19686 "],"isi":["001459780300005"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes"},{"article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"external_id":{"isi":["001516570500009"]},"oa_version":"Published Version","title":"STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 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.","ddc":["570"],"department":[{"_id":"AnSa"}],"date_published":"2025-06-18T00:00:00Z","date_created":"2025-06-15T22:01:31Z","file":[{"creator":"dernst","file_name":"2025_CellReportsPhysicalScience_Najjar.pdf","checksum":"37ff7c396f966d0ec363e4691d63d402","success":1,"date_created":"2025-06-23T10:20:22Z","access_level":"open_access","file_id":"19868","date_updated":"2025-06-23T10:20:22Z","content_type":"application/pdf","relation":"main_file","file_size":9771117}],"_id":"19846","has_accepted_license":"1","month":"06","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2666-3864"]},"quality_controlled":"1","status":"public","year":"2025","abstract":[{"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.","lang":"eng"}],"fulldoi":"https://doi.org/10.1016/j.xcrp.2025.102623","file_date_updated":"2025-06-23T10:20:22Z","OA_place":"publisher","publication_status":"published","day":"18","author":[{"first_name":"Hadil","full_name":"Najjar, Hadil","last_name":"Najjar"},{"last_name":"Weiß","full_name":"Weiß, Sarah","first_name":"Sarah"},{"first_name":"Ferdinand","id":"b0dc7f61-21a3-11ef-a9b4-e6ab1aa6f21e","full_name":"Horvath, Ferdinand","last_name":"Horvath"},{"last_name":"Hopl","full_name":"Hopl, Valentina","first_name":"Valentina"},{"first_name":"Adéla","full_name":"Tiffner, Adéla","last_name":"Tiffner"},{"full_name":"Höbarth, Lorenz","first_name":"Lorenz","last_name":"Höbarth"},{"first_name":"Julia","full_name":"Söllner, Julia","last_name":"Söllner"},{"last_name":"Fröhlich","full_name":"Fröhlich, Maximilian","first_name":"Maximilian"},{"last_name":"Prantl","full_name":"Prantl, Magdalena","first_name":"Magdalena"},{"first_name":"Nora","full_name":"Müller, Nora","last_name":"Müller"},{"last_name":"Nazarenko","first_name":"Yuliia","full_name":"Nazarenko, Yuliia"},{"first_name":"Selina","full_name":"Harant, Selina","last_name":"Harant"},{"full_name":"Weissenböck, Lukas","first_name":"Lukas","last_name":"Weissenböck"},{"first_name":"Herwig","full_name":"Grabmayr, Herwig","last_name":"Grabmayr"},{"last_name":"Sallinger","first_name":"Matthias","full_name":"Sallinger, Matthias"},{"first_name":"Lena","full_name":"Maltan, Lena","last_name":"Maltan"},{"full_name":"Echefu, Linda V.","first_name":"Linda V.","last_name":"Echefu"},{"full_name":"Radiskovic, Tamara","first_name":"Tamara","last_name":"Radiskovic"},{"last_name":"Leopold","full_name":"Leopold, Melanie","first_name":"Melanie"},{"first_name":"Sonja","full_name":"Lindinger, Sonja","last_name":"Lindinger"},{"last_name":"Humer","full_name":"Humer, Christina","first_name":"Christina"},{"full_name":"Höglinger, Carmen","first_name":"Carmen","last_name":"Höglinger"},{"last_name":"Krobath","first_name":"Heinrich","full_name":"Krobath, Heinrich"},{"first_name":"Thomas","full_name":"Renger, Thomas","last_name":"Renger"},{"last_name":"Derler","first_name":"Isabella","full_name":"Derler, Isabella"}],"OA_type":"gold","article_type":"original","doi":"10.1016/j.xcrp.2025.102623","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-09-30T12:53:15Z","intvolume":" 6","oa":1,"scopus_import":"1","publisher":"Elsevier","issue":"6","publication":"Cell Reports Physical Science","volume":6,"type":"journal_article","DOAJ_listed":"1","article_number":"102623","citation":{"mla":"Najjar, Hadil, et al. “STIM1-Induced Widening of Non-Pore-Lining TM Interfaces Is Crucial for Orai1 Pore Opening.” Cell Reports Physical Science, vol. 6, no. 6, 102623, Elsevier, 2025, doi:10.1016/j.xcrp.2025.102623.","ama":"Najjar H, Weiß S, Horvath F, et al. STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening. Cell Reports Physical Science. 2025;6(6). doi:10.1016/j.xcrp.2025.102623","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.","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).","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.” Cell Reports Physical Science. Elsevier, 2025. https://doi.org/10.1016/j.xcrp.2025.102623.","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. Cell Reports Physical Science. Elsevier. https://doi.org/10.1016/j.xcrp.2025.102623","ieee":"H. Najjar et al., “STIM1-induced widening of non-pore-lining TM interfaces is crucial for Orai1 pore opening,” Cell Reports Physical Science, vol. 6, no. 6. Elsevier, 2025."}},{"date_updated":"2025-12-30T08:41:57Z","intvolume":" 37","PlanS_conform":"1","doi":"10.1021/acs.chemmater.5c00213","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","publisher":"American Chemical Society","oa":1,"publication":"Chemistry of Materials","volume":37,"type":"journal_article","issue":"12","citation":{"mla":"Palacios Corella, Mario, et al. “Prussian Blue Analogues as Anode Materials for Battery Applications: Complexities and Horizons.” Chemistry of Materials, vol. 37, no. 12, American Chemical Society, 2025, pp. 4203–26, doi:10.1021/acs.chemmater.5c00213.","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. Chemistry of Materials. 2025;37(12):4203-4226. doi:10.1021/acs.chemmater.5c00213","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.","short":"M. Palacios Corella, I. Echevarría, C. Santana Santos, W. Schuhmann, E. Ventosa, M. Ibáñez, Chemistry of Materials 37 (2025) 4203–4226.","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.” Chemistry of Materials. American Chemical Society, 2025. https://doi.org/10.1021/acs.chemmater.5c00213.","apa":"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. American Chemical Society. https://doi.org/10.1021/acs.chemmater.5c00213","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,” Chemistry of Materials, vol. 37, no. 12. American Chemical Society, pp. 4203–4226, 2025."},"fulldoi":"https://doi.org/10.1021/acs.chemmater.5c00213","corr_author":"1","OA_place":"publisher","file_date_updated":"2025-12-30T08:40:55Z","abstract":[{"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.","lang":"eng"}],"publication_status":"published","day":"03","OA_type":"hybrid","author":[{"id":"452e82c6-803f-11ed-ab7e-ca0439e73a5d","first_name":"Mario","full_name":"Palacios Corella, Mario","last_name":"Palacios Corella"},{"last_name":"Echevarría","first_name":"Igor","id":"a623795e-21fb-11ed-b8a1-a0f51308eed7","full_name":"Echevarría, Igor"},{"full_name":"Santana Santos, Carla","first_name":"Carla","last_name":"Santana Santos"},{"last_name":"Schuhmann","first_name":"Wolfgang","full_name":"Schuhmann, Wolfgang"},{"first_name":"Edgar","full_name":"Ventosa, Edgar","last_name":"Ventosa"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"article_type":"original","_id":"19847","publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"06","page":"4203-4226","status":"public","quality_controlled":"1","year":"2025","project":[{"_id":"eb9fa02e-77a9-11ec-83b8-ab1143e5a30f","grant_number":"101046742","name":"MEDIATED BIPHASIC BATTERY"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","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).","title":"Prussian blue analogues as anode materials for battery applications: Complexities and horizons","isi":1,"external_id":{"isi":["001501830600001"]},"department":[{"_id":"MaIb"}],"ddc":["540"],"file":[{"creator":"dernst","file_name":"2025_ChemistryMaterials_PalaciosCorella.pdf","checksum":"902c52a2f52a028436e0acd8a5a4beac","success":1,"date_created":"2025-12-30T08:40:55Z","access_level":"open_access","file_id":"20897","date_updated":"2025-12-30T08:40:55Z","content_type":"application/pdf","relation":"main_file","file_size":8760757}],"date_created":"2025-06-15T22:01:31Z","date_published":"2025-06-03T00:00:00Z"},{"publication_identifier":{"issn":["0924-8463"],"eissn":["1572-8382"]},"language":[{"iso":"eng"}],"month":"05","_id":"19848","status":"public","quality_controlled":"1","year":"2025","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10506-025-09458-6"}],"oa_version":"Published Version","title":"Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","isi":1,"external_id":{"isi":["001494836700001"],"arxiv":["2407.07004"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","date_created":"2025-06-15T22:01:31Z","date_published":"2025-05-26T00:00:00Z","department":[{"_id":"UlWa"}],"ddc":["510"],"scopus_import":"1","publisher":"Springer Nature","oa":1,"date_updated":"2026-06-18T08:34:38Z","doi":"10.1007/s10506-025-09458-6","citation":{"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. Artificial Intelligence and Law. 2025. doi:10.1007/s10506-025-09458-6","mla":"Tinarrage, Raphaël, et al. “Empirical Analysis of Binding Precedent Efficiency in Brazilian Supreme Court via Case Classification.” Artificial Intelligence and Law, Springer Nature, 2025, doi:10.1007/s10506-025-09458-6.","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.","short":"R. Tinarrage, H. Ennes, L. Resck, L.T. Gomes, J.R. Ponciano, J. Poco, Artificial Intelligence and Law (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.” Artificial Intelligence and Law. Springer Nature, 2025. https://doi.org/10.1007/s10506-025-09458-6.","apa":"Tinarrage, R., Ennes, H., Resck, L., Gomes, L. T., Ponciano, J. R., & Poco, J. (2025). Empirical analysis of binding precedent efficiency in Brazilian Supreme Court via case classification. Artificial Intelligence and Law. Springer Nature. https://doi.org/10.1007/s10506-025-09458-6","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,” Artificial Intelligence and Law. Springer Nature, 2025."},"publication":"Artificial Intelligence and Law","type":"journal_article","day":"26","arxiv":1,"publication_status":"epub_ahead","fulldoi":"https://doi.org/10.1007/s10506-025-09458-6","OA_place":"publisher","corr_author":"1","abstract":[{"lang":"eng","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."}],"article_type":"original","OA_type":"hybrid","author":[{"full_name":"Tinarrage, Raphaël","first_name":"Raphaël","id":"40ebcc9d-905f-11ef-bf0a-dc475da8a04e","orcid":"0000-0002-1404-1095","last_name":"Tinarrage"},{"first_name":"Henrique","full_name":"Ennes, Henrique","last_name":"Ennes"},{"last_name":"Resck","first_name":"Lucas","full_name":"Resck, Lucas"},{"first_name":"Lucas T.","full_name":"Gomes, Lucas T.","last_name":"Gomes"},{"last_name":"Ponciano","first_name":"Jean R.","full_name":"Ponciano, Jean R."},{"last_name":"Poco","first_name":"Jorge","full_name":"Poco, Jorge"}]},{"publication_status":"published","arxiv":1,"day":"18","corr_author":"1","OA_place":"publisher","file_date_updated":"2025-06-23T10:31:11Z","fulldoi":"https://doi.org/10.1103/k4jh-pnxy","abstract":[{"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.","lang":"eng"}],"article_type":"original","OA_type":"hybrid","author":[{"last_name":"Babkin","first_name":"Serafim","id":"e63d75c3-72ef-11ef-b75a-e303e149911f","full_name":"Babkin, Serafim"},{"first_name":"Benjamin","full_name":"Joecker, Benjamin","last_name":"Joecker"},{"first_name":"Karsten","full_name":"Flensberg, Karsten","last_name":"Flensberg"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Danon","first_name":"Jeroen","full_name":"Danon, Jeroen"}],"publisher":"American Physical Society","scopus_import":"1","oa":1,"intvolume":" 111","date_updated":"2025-09-30T12:53:47Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1103/k4jh-pnxy","citation":{"apa":"Babkin, S., Joecker, B., Flensberg, K., Serbyn, M., & Danon, J. (2025). Superconducting proximity effect in two-dimensional hole gases. Physical Review B. American Physical Society. https://doi.org/10.1103/k4jh-pnxy","ieee":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, and J. Danon, “Superconducting proximity effect in two-dimensional hole gases,” Physical Review B, vol. 111, no. 21. American Physical Society, 2025.","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.","short":"S. Babkin, B. Joecker, K. Flensberg, M. Serbyn, J. Danon, Physical Review B 111 (2025).","mla":"Babkin, Serafim, et al. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” Physical Review B, vol. 111, no. 21, 214518, American Physical Society, 2025, doi:10.1103/k4jh-pnxy.","ama":"Babkin S, Joecker B, Flensberg K, Serbyn M, Danon J. Superconducting proximity effect in two-dimensional hole gases. Physical Review B. 2025;111(21). doi:10.1103/k4jh-pnxy","chicago":"Babkin, Serafim, Benjamin Joecker, Karsten Flensberg, Maksym Serbyn, and Jeroen Danon. “Superconducting Proximity Effect in Two-Dimensional Hole Gases.” Physical Review B. American Physical Society, 2025. https://doi.org/10.1103/k4jh-pnxy."},"article_number":"214518","type":"journal_article","volume":111,"publication":"Physical Review B","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.","title":"Superconducting proximity effect in two-dimensional hole gases","oa_version":"Published Version","external_id":{"arxiv":["2412.04084"],"isi":["001514328000004"]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","date_created":"2025-06-19T16:54:54Z","file":[{"content_type":"application/pdf","date_updated":"2025-06-23T10:31:11Z","file_id":"19869","access_level":"open_access","file_size":1719489,"relation":"main_file","file_name":"2025_PhysReviewB_Babkin.pdf","creator":"dernst","date_created":"2025-06-23T10:31:11Z","success":1,"checksum":"fa8757f4780cfaeb51579c626284a8c1"}],"date_published":"2025-06-18T00:00:00Z","department":[{"_id":"MaSe"},{"_id":"GradSch"}],"ddc":["530"],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"06","has_accepted_license":"1","_id":"19852","project":[{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Probing topology in circuits and quantum materials","grant_number":"F8609","_id":"34a7f947-11ca-11ed-8bc3-c5dc2bbaae25"}],"year":"2025","quality_controlled":"1","status":"public"},{"page":"38","status":"public","year":"2025","_id":"19853","has_accepted_license":"1","month":"10","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"ddc":["520"],"department":[{"_id":"GradSch"},{"_id":"LiBu"}],"date_published":"2025-10-08T00:00:00Z","file":[{"access_level":"closed","date_updated":"2025-10-08T09:45:33Z","content_type":"application/zip","file_id":"20434","file_size":8263624,"relation":"source_file","creator":"ksmith","file_name":"2025_Smith_Kanah_Thesis.zip","checksum":"80d241d11b69af771c1fab0998be4f19","date_created":"2025-10-08T08:01:42Z"},{"relation":"main_file","file_size":9748339,"file_id":"20439","content_type":"application/pdf","date_updated":"2025-10-09T14:38:57Z","access_level":"open_access","success":1,"date_created":"2025-10-09T14:38:57Z","checksum":"13cb48cc98e00fdfe32f3ff66f17aa26","file_name":"2025_Smith_Kanah_Thesis.pdf","creator":"ksmith"}],"date_created":"2025-06-20T13:27:08Z","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","acknowledgement":"I would like to give thanks to myself for my hard work on this document. This paper includes data collected by the Kepler mission and obtained from the MAST data\r\narchive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is\r\nprovided by the NASA Science Mission Directorate. STScI is operated by the Association of\r\nUniversities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.\r\n","title":"Exploring internal magnetism in partially suppressed red giant stars","type":"dissertation","alternative_title":["ISTA Master's Thesis"],"citation":{"chicago":"Smith, Kanah. “Exploring Internal Magnetism in Partially Suppressed Red Giant Stars.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19853.","short":"K. Smith, Exploring Internal Magnetism in Partially Suppressed Red Giant Stars, Institute of Science and Technology Austria, 2025.","ista":"Smith K. 2025. Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria.","ama":"Smith K. Exploring internal magnetism in partially suppressed red giant stars. 2025. doi:10.15479/AT-ISTA-19853","mla":"Smith, Kanah. Exploring Internal Magnetism in Partially Suppressed Red Giant Stars. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19853.","ieee":"K. Smith, “Exploring internal magnetism in partially suppressed red giant stars,” Institute of Science and Technology Austria, 2025.","apa":"Smith, K. (2025). Exploring internal magnetism in partially suppressed red giant stars. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19853"},"doi":"10.15479/AT-ISTA-19853","date_updated":"2026-04-07T12:01:37Z","degree_awarded":"MS","oa":1,"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Kanah","id":"7703505d-3211-11ee-a6a9-a2ab9d936c15","full_name":"Smith, Kanah","last_name":"Smith"}],"abstract":[{"text":"The internal dynamical properties of red giant stars have been explored extensively in recent\r\nyears as a result of the increase in high precision data availability from the space missions\r\nKepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been\r\ndiscovered that some of these stars are not behaving as expected. Red giants are stars that have\r\nevolved off of the main sequence after having completed fusing hydrogen into helium in their\r\ncore. Observational data shows that the cores are rotating significantly slower than models can\r\nrecreate consistently across evolutionary stages. This discrepancy has prompted investigation\r\ninto the efficiency of angular momentum transport mechanisms and mixing processes including\r\nmeridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil\r\nmagnetic fields etc., to explain this behavior.\r\nAnalyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only\r\nway in which the deep stellar interior can be probed and subsequently characterized; this is\r\npossible as global oscillations modulating the stellar surface are effected by internal processes.\r\nFor red giants, p-modes (pressure modes; resonating through the entire star) and g-modes\r\n(gravity-modes; resonating in the radiative interior) couple to create mixed modes. These\r\nmixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes,\r\ndelivering information from the interior to the surface.\r\nInternal magnetic signatures have been observationally confirmed in red giant stars via\r\nasteroseismology and characterized in two ways. One being that dipole mixed modes with\r\nℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where\r\nthe m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two\r\ndifferent power laws, respectively. And the other being a reduced visibility of dipole mixed\r\nmode amplitudes in the power spectra, where stars presenting with this feature are denoted as\r\nsuppressed.\r\nSeveral studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus\r\nfar, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been\r\nconducted; one reason being that the asymmetric frequency shifts cannot be characterized\r\nwhen the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars.\r\nSincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed\r\nstars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of\r\ntheir power spectra rather than across the entire spectra, will be the subject of this study as\r\nthe respective mode amplitudes are still visible at high frequencies.\r\nAs such, this study will search for asymmetric frequency shifts on the dipole mixed\r\nmodes of partially suppressed red giant stars; the aim here is to investigate if both\r\nmode suppression and magnetic shifting of dipole mixed modes occur simultaneously.\r\nThisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters,\r\nuse the priors to model the power spectra with the stellar modeling code sloscillations_ISTA,\r\nand perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038,\r\na target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its\r\nmagnetic parameters. I present a novel method to model the stellar power spectra of\r\npartially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar\r\nmode component of the spectra. With the results of this study I aim at constraining\r\nthe cause of this partial dipole mode amplitude suppression, allowing for more detailed\r\nstudies regarding their astrophysical nature. Furthermore, the long term hope for the method\r\nused in this study will be to expand the sample of partially suppressed red giants and fit their\r\nasteroseismic parameters accordingly.","lang":"eng"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-19853","corr_author":"1","supervisor":[{"id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","last_name":"Bugnet"}],"OA_place":"publisher","file_date_updated":"2025-10-09T14:38:57Z","keyword":["asteroseismology","stellar physics","red giant","magnetism","suppressed"],"day":"08","publication_status":"published"},{"type":"journal_article","volume":91,"publication":"Journal of Mathematical Biology","citation":{"apa":"Pastva, S., Park, K. H., Huvar, O., Rozum, J. C., & Albert, R. (2025). An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks? Journal of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s00285-025-02235-8","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?,” Journal of Mathematical Biology, vol. 91. Springer Nature, 2025.","short":"S. Pastva, K.H. Park, O. Huvar, J.C. Rozum, R. Albert, Journal of Mathematical Biology 91 (2025).","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.","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? Journal of Mathematical Biology. 2025;91. doi:10.1007/s00285-025-02235-8","mla":"Pastva, Samuel, et al. “An Open Problem: Why Are Motif-Avoidant Attractors so Rare in Asynchronous Boolean Networks?” Journal of Mathematical Biology, vol. 91, 11, Springer Nature, 2025, doi:10.1007/s00285-025-02235-8.","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?” Journal of Mathematical Biology. Springer Nature, 2025. https://doi.org/10.1007/s00285-025-02235-8."},"article_number":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1007/s00285-025-02235-8","intvolume":" 91","date_updated":"2025-09-30T13:36:46Z","oa":1,"publisher":"Springer Nature","scopus_import":"1","author":[{"last_name":"Pastva","orcid":"0000-0003-1993-0331","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"},{"first_name":"Kyu Hyong","full_name":"Park, Kyu Hyong","last_name":"Park"},{"last_name":"Huvar","full_name":"Huvar, Ondřej","first_name":"Ondřej"},{"last_name":"Rozum","first_name":"Jordan C.","full_name":"Rozum, Jordan C."},{"first_name":"Réka","full_name":"Albert, Réka","last_name":"Albert"}],"OA_type":"hybrid","article_type":"original","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"}],"file_date_updated":"2025-06-23T11:10:01Z","OA_place":"publisher","corr_author":"1","fulldoi":"https://doi.org/10.1007/s00285-025-02235-8","arxiv":1,"publication_status":"published","day":"12","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"quality_controlled":"1","year":"2025","status":"public","_id":"19854","ec_funded":1,"month":"06","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0303-6812"],"eissn":["1432-1416"]},"ddc":["000"],"department":[{"_id":"ToHe"}],"date_published":"2025-06-12T00:00:00Z","date_created":"2025-06-22T22:02:05Z","file":[{"file_size":1243163,"relation":"main_file","date_updated":"2025-06-23T11:10:01Z","content_type":"application/pdf","file_id":"19871","access_level":"open_access","date_created":"2025-06-23T11:10:01Z","success":1,"checksum":"a385ef2662f1d0c3497ed3f2721fe594","file_name":"2025_JourMathBiology_Pastva.pdf","creator":"dernst"}],"article_processing_charge":"Yes (in subscription journal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2410.03976"],"isi":["001507009300001"]},"isi":1,"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.","title":"An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?","oa_version":"Published Version"},{"ddc":["520"],"department":[{"_id":"JoMa"}],"date_published":"2025-07-01T00:00:00Z","date_created":"2025-06-22T22:02:05Z","file":[{"date_created":"2025-06-23T11:02:59Z","success":1,"checksum":"f912c990a0474f1ddf9be6b8a89c7759","file_name":"2025_MonthlyNoticesRAS_Gazagnes.pdf","creator":"dernst","relation":"main_file","file_size":3111567,"content_type":"application/pdf","date_updated":"2025-06-23T11:02:59Z","file_id":"19870","access_level":"open_access"}],"article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001506103600001"],"arxiv":["2410.03337"]},"isi":1,"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.","title":"A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization","oa_version":"Published Version","page":"2331-2348","year":"2025","quality_controlled":"1","status":"public","_id":"19855","month":"07","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"author":[{"first_name":"S.","full_name":"Gazagnes, S.","last_name":"Gazagnes"},{"first_name":"J.","full_name":"Chisholm, J.","last_name":"Chisholm"},{"last_name":"Endsley","first_name":"R.","full_name":"Endsley, R."},{"last_name":"Berg","full_name":"Berg, D. A.","first_name":"D. A."},{"last_name":"Leclercq","full_name":"Leclercq, F.","first_name":"F."},{"last_name":"Jurlin","first_name":"N.","full_name":"Jurlin, N."},{"last_name":"Saldana-Lopez","first_name":"A.","full_name":"Saldana-Lopez, A."},{"last_name":"Finkelstein","first_name":"S. L.","full_name":"Finkelstein, S. L."},{"full_name":"Flury, S. R.","first_name":"S. R.","last_name":"Flury"},{"last_name":"Guseva","first_name":"N. G.","full_name":"Guseva, N. G."},{"first_name":"A.","full_name":"Henry, A.","last_name":"Henry"},{"first_name":"Y. I.","full_name":"Izotov, Y. I.","last_name":"Izotov"},{"last_name":"Jung","first_name":"I.","full_name":"Jung, I."},{"last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"last_name":"Schaerer","full_name":"Schaerer, D.","first_name":"D."}],"OA_type":"gold","article_type":"original","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."}],"file_date_updated":"2025-06-23T11:02:59Z","OA_place":"publisher","fulldoi":"https://doi.org/10.1093/mnras/staf768","publication_status":"published","arxiv":1,"day":"01","issue":"3","type":"journal_article","publication":"Monthly Notices of the Royal Astronomical Society","volume":540,"citation":{"ieee":"S. Gazagnes et al., “A negligible contribution of two luminous z ∼7.5 galaxies to the ionizing photon budget of reionization,” Monthly Notices of the Royal Astronomical Society, 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. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staf768","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.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2025. https://doi.org/10.1093/mnras/staf768.","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.","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.","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. Monthly Notices of the Royal Astronomical Society. 2025;540(3):2331-2348. doi:10.1093/mnras/staf768","mla":"Gazagnes, S., et al. “A Negligible Contribution of Two Luminous z ∼7.5 Galaxies to the Ionizing Photon Budget of Reionization.” Monthly Notices of the Royal Astronomical Society, vol. 540, no. 3, Oxford University Press, 2025, pp. 2331–48, doi:10.1093/mnras/staf768."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1093/mnras/staf768","date_updated":"2025-09-30T13:34:20Z","intvolume":" 540","oa":1,"scopus_import":"1","publisher":"Oxford University Press"},{"status":"public","quality_controlled":"1","year":"2025","month":"06","has_accepted_license":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"_id":"19856","date_published":"2025-06-13T00:00:00Z","date_created":"2025-06-22T22:02:06Z","file":[{"file_size":1132625,"relation":"main_file","content_type":"application/pdf","date_updated":"2025-06-23T11:41:08Z","file_id":"19874","access_level":"open_access","date_created":"2025-06-23T11:41:08Z","success":1,"checksum":"040b6779c91aac62c15a9b2cc417b360","file_name":"2025_PhysReviewLetters_Zu.pdf","creator":"dernst"}],"ddc":["530"],"department":[{"_id":"CaGo"},{"_id":"IlCa"}],"external_id":{"isi":["001509005900006"],"arxiv":["2412.05031"]},"isi":1,"acknowledgement":"We gratefully acknowledge Edouard Hannezo for helpful comments on the manuscript. The work was funded by the Institute of Science and Technology Austria.","title":"Fully independent response in disordered solids","related_material":{"link":[{"url":"https://ista.ac.at/en/news/infinite-diversity-in-infinite-combinations/","relation":"press_release","description":"News on ISTA website"}]},"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Zu, M., Desai, A. A., & Goodrich, C. P. (2025). Fully independent response in disordered solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.238201","ieee":"M. Zu, A. A. Desai, and C. P. Goodrich, “Fully independent response in disordered solids,” Physical Review Letters, vol. 134, no. 23. American Physical Society, 2025.","mla":"Zu, Mengjie, et al. “Fully Independent Response in Disordered Solids.” Physical Review Letters, vol. 134, no. 23, 238201, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.238201.","ama":"Zu M, Desai AA, Goodrich CP. Fully independent response in disordered solids. Physical Review Letters. 2025;134(23). doi:10.1103/PhysRevLett.134.238201","short":"M. Zu, A.A. Desai, C.P. Goodrich, Physical Review Letters 134 (2025).","ista":"Zu M, Desai AA, Goodrich CP. 2025. Fully independent response in disordered solids. Physical Review Letters. 134(23), 238201.","chicago":"Zu, Mengjie, Aayush A Desai, and Carl Peter Goodrich. “Fully Independent Response in Disordered Solids.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.238201."},"article_number":"238201","issue":"23","type":"journal_article","publication":"Physical Review Letters","volume":134,"oa":1,"publisher":"American Physical Society","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1103/PhysRevLett.134.238201","date_updated":"2026-04-28T13:28:02Z","intvolume":" 134","article_type":"original","author":[{"full_name":"Zu, Mengjie","first_name":"Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","last_name":"Zu"},{"id":"502cfd30-32c1-11ee-a9a4-d8dad5c6739e","first_name":"Aayush A","full_name":"Desai, Aayush A","last_name":"Desai"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich"}],"OA_type":"hybrid","arxiv":1,"day":"13","publication_status":"published","abstract":[{"text":"Unlike in crystals, it is difficult to trace emergent material properties of amorphous solids to their underlying structure. Nevertheless, one can tune features of a disordered spring network, ranging from bulk elastic constants to specific allosteric responses, through highly precise alterations of the structure. This has been understood through the notion of independent bond-level response—the observation that, in many cases, different springs have different effects on different properties. While this idea has motivated inverse design in numerous contexts, it has not been formalized and quantified in a general context that not just informs but enables and predicts inverse design. Here, we show how to quantify independent response by linearizing the simultaneous change in multiple emergent features, and introduce the much stronger notion of fully independent response. Remarkably, we find that the mechanical properties of disordered solids are always fully independent across a wide array of scenarios, regardless of the target features, tunable parameters, system size, dimensionality, and class of interactions. Furthermore, our formulation quantifies the susceptibility of features to parameter changes, which is correlated with the maximum linear tunability. We also demonstrate the implications for multifeature inverse design beyond the linear regime. These results formalize our understanding of a key fundamental difference between ordered and disordered solids while also creating a practical tool to both understand and perform inverse design.","lang":"eng"}],"corr_author":"1","file_date_updated":"2025-06-23T11:41:08Z","OA_place":"publisher","fulldoi":"https://doi.org/10.1103/PhysRevLett.134.238201"},{"citation":{"apa":"Nikolic, N., Pleska, M., Bergmiller, T., & Guet, C. C. (2025). A bacterial toxin-antitoxin system as a native defence element against RNA phages. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2025.0080","ieee":"N. Nikolic, M. Pleska, T. Bergmiller, and C. C. Guet, “A bacterial toxin-antitoxin system as a native defence element against RNA phages,” Biology Letters, vol. 21, no. 6. The Royal Society, 2025.","ama":"Nikolic N, Pleska M, Bergmiller T, Guet CC. A bacterial toxin-antitoxin system as a native defence element against RNA phages. Biology Letters. 2025;21(6). doi:10.1098/rsbl.2025.0080","mla":"Nikolic, Nela, et al. “A Bacterial Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” Biology Letters, vol. 21, no. 6, 20250080, The Royal Society, 2025, doi:10.1098/rsbl.2025.0080.","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.","short":"N. Nikolic, M. Pleska, T. Bergmiller, C.C. Guet, Biology Letters 21 (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.” Biology Letters. The Royal Society, 2025. https://doi.org/10.1098/rsbl.2025.0080."},"article_number":"20250080","issue":"6","type":"journal_article","publication":"Biology Letters","volume":21,"pmid":1,"oa":1,"publisher":"The Royal Society","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1098/rsbl.2025.0080","date_updated":"2025-09-30T13:38:08Z","intvolume":" 21","article_type":"original","author":[{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela"},{"last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479"},{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"}],"OA_type":"hybrid","day":"11","publication_status":"published","abstract":[{"lang":"eng","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."}],"file_date_updated":"2025-06-23T11:34:39Z","corr_author":"1","OA_place":"publisher","fulldoi":"https://doi.org/10.1098/rsbl.2025.0080","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","call_identifier":"FWF","_id":"26956E74-B435-11E9-9278-68D0E5697425","grant_number":"V00738"}],"quality_controlled":"1","status":"public","year":"2025","month":"06","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-9561"],"eissn":["1744-957X"]},"_id":"19857","ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2025-06-11T00:00:00Z","file":[{"file_size":1850797,"relation":"main_file","access_level":"open_access","date_updated":"2025-06-23T11:34:39Z","content_type":"application/pdf","file_id":"19873","checksum":"016f644ed068f8609ded306ad26dbd3f","date_created":"2025-06-23T11:34:39Z","success":1,"creator":"dernst","file_name":"2025_BiologyLetters_Nikolic.pdf"}],"date_created":"2025-06-22T22:02:06Z","ddc":["570"],"department":[{"_id":"CaGu"}],"external_id":{"pmid":["40494395"],"isi":["001505019800001"]},"isi":1,"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.","title":"A bacterial toxin-antitoxin system as a native defence element against RNA phages","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"citation":{"mla":"El-Hayek, Antoine, et al. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” 4th Symposium on Algorithmic Foundations of Dynamic Networks, vol. 330, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, doi:10.4230/LIPIcs.SAND.2025.4.","ama":"El-Hayek A, Hanauer K, Henzinger M. On b-matching and fully-dynamic maximum k-edge coloring. In: 4th Symposium on Algorithmic Foundations of Dynamic Networks. Vol 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025. doi:10.4230/LIPIcs.SAND.2025.4","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.","short":"A. El-Hayek, K. Hanauer, M. Henzinger, in:, 4th Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025.","chicago":"El-Hayek, Antoine, Kathrin Hanauer, and Monika Henzinger. “On B-Matching and Fully-Dynamic Maximum k-Edge Coloring.” In 4th Symposium on Algorithmic Foundations of Dynamic Networks, Vol. 330. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. https://doi.org/10.4230/LIPIcs.SAND.2025.4.","apa":"El-Hayek, A., Hanauer, K., & Henzinger, M. (2025). On b-matching and fully-dynamic maximum k-edge coloring. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (Vol. 330). Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SAND.2025.4","ieee":"A. El-Hayek, K. Hanauer, and M. Henzinger, “On b-matching and fully-dynamic maximum k-edge coloring,” in 4th Symposium on Algorithmic Foundations of Dynamic Networks, Liverpool, United Kingdom, 2025, vol. 330."},"alternative_title":["LIPIcs"],"article_number":"4","type":"conference","volume":330,"publication":"4th Symposium on Algorithmic Foundations of Dynamic Networks","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","oa":1,"intvolume":" 330","date_updated":"2025-09-30T13:37:28Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.4230/LIPIcs.SAND.2025.4","OA_type":"gold","author":[{"last_name":"El-Hayek","orcid":"0000-0003-4268-7368","first_name":"Antoine","full_name":"El-Hayek, Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725"},{"full_name":"Hanauer, Kathrin","first_name":"Kathrin","last_name":"Hanauer"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger"}],"day":"02","conference":{"start_date":"2025-06-09","end_date":"2025-06-11","name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","location":"Liverpool, United Kingdom"},"publication_status":"published","arxiv":1,"OA_place":"publisher","file_date_updated":"2025-06-23T11:23:29Z","corr_author":"1","fulldoi":"https://doi.org/10.4230/LIPIcs.SAND.2025.4","abstract":[{"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.","lang":"eng"}],"project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Efficient algorithms","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"quality_controlled":"1","status":"public","year":"2025","publication_identifier":{"isbn":["9783959773683"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"month":"06","has_accepted_license":"1","ec_funded":1,"_id":"19858","file":[{"creator":"dernst","file_name":"2025_LIPIcs_ElHayek.pdf","checksum":"ad93a1e052adb29d7bfe8bd551bab193","success":1,"date_created":"2025-06-23T11:23:29Z","access_level":"open_access","file_id":"19872","date_updated":"2025-06-23T11:23:29Z","content_type":"application/pdf","file_size":995666,"relation":"main_file"}],"date_created":"2025-06-22T22:02:06Z","date_published":"2025-06-02T00:00:00Z","department":[{"_id":"MoHe"}],"ddc":["000"],"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.","title":"On b-matching and fully-dynamic maximum k-edge coloring","oa_version":"Published Version","external_id":{"arxiv":["2310.01149"],"isi":["001532136900004"]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No"},{"external_id":{"arxiv":["2211.16086 "]},"title":"Color-avoiding percolation on the Erdős–Rényi random graph","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.","oa_version":"Published Version","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-06-01T00:00:00Z","date_created":"2025-06-22T22:02:07Z","file":[{"creator":"dernst","file_name":"2025_AnnalesHenriLebesgue_Lichev.pdf","checksum":"cca22d171b7affa010d17f5e793b0045","success":1,"date_created":"2025-06-23T11:59:22Z","access_level":"open_access","file_id":"19875","content_type":"application/pdf","date_updated":"2025-06-23T11:59:22Z","file_size":746588,"relation":"main_file"}],"ddc":["510"],"department":[{"_id":"MaKw"}],"month":"06","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2644-9463"]},"_id":"19859","year":"2025","quality_controlled":"1","status":"public","page":"35-65","day":"01","publication_status":"published","arxiv":1,"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2025-06-23T11:59:22Z","OA_place":"publisher","corr_author":"1","fulldoi":"https://doi.org/10.5802/ahl.228","article_type":"original","author":[{"last_name":"Lichev","first_name":"Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977","full_name":"Lichev, Lyuben"},{"last_name":"Schapira","first_name":"Bruno","full_name":"Schapira, Bruno"}],"OA_type":"gold","oa":1,"scopus_import":"1","publisher":"École normale supérieure de Rennes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.5802/ahl.228","intvolume":" 8","date_updated":"2025-06-23T12:01:36Z","citation":{"chicago":"Lichev, Lyuben, and Bruno Schapira. “Color-Avoiding Percolation on the Erdős–Rényi Random Graph.” Annales Henri Lebesgue. École normale supérieure de Rennes, 2025. https://doi.org/10.5802/ahl.228.","short":"L. Lichev, B. Schapira, Annales Henri Lebesgue 8 (2025) 35–65.","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.” Annales Henri Lebesgue, vol. 8, École normale supérieure de Rennes, 2025, pp. 35–65, doi:10.5802/ahl.228.","ama":"Lichev L, Schapira B. Color-avoiding percolation on the Erdős–Rényi random graph. Annales Henri Lebesgue. 2025;8:35-65. doi:10.5802/ahl.228","ieee":"L. Lichev and B. Schapira, “Color-avoiding percolation on the Erdős–Rényi random graph,” Annales Henri Lebesgue, vol. 8. École normale supérieure de Rennes, pp. 35–65, 2025.","apa":"Lichev, L., & Schapira, B. (2025). Color-avoiding percolation on the Erdős–Rényi random graph. Annales Henri Lebesgue. École normale supérieure de Rennes. https://doi.org/10.5802/ahl.228"},"type":"journal_article","DOAJ_listed":"1","publication":"Annales Henri Lebesgue","volume":8}]