[{"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"month":"04","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"page":"124","citation":{"ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>.","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025.","ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria."},"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"file_date_updated":"2026-03-27T13:15:08Z","ddc":["570"],"degree_awarded":"PhD","corr_author":"1","_id":"19557","status":"public","date_updated":"2026-04-14T09:07:14Z","related_material":{"record":[{"id":"12802","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9429"}]},"file":[{"file_id":"19561","file_name":"Schwarz_Thesis_2025_FINAL.docx","relation":"source_file","access_level":"closed","checksum":"50290a8604edb0a720387f01e9d59fe4","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-04-15T08:43:36Z","file_size":21783427,"creator":"lschwarz","date_updated":"2025-04-15T08:43:36Z"},{"access_level":"closed","embargo":"2026-10-15","relation":"main_file","file_id":"19562","file_name":"Schwarz_Thesis_2025_FINALpdfa.pdf","checksum":"ed028488180ac4901e018ef1c330cf01","embargo_to":"open_access","file_size":11432175,"date_created":"2025-04-15T08:43:42Z","content_type":"application/pdf","date_updated":"2026-03-27T13:15:08Z","creator":"lschwarz"}],"date_published":"2025-04-14T00:00:00Z","day":"14","author":[{"first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A","last_name":"Schwarz"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution","type":"dissertation","project":[{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","grant_number":"101044865","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"year":"2025","doi":"10.15479/AT-ISTA-19557","acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","date_created":"2025-04-14T06:59:06Z","alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"publication_status":"published","article_type":"original","title":"Multivariate Gini-type discrepancies","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-04-15T13:34:00Z","doi":"10.1142/s0218202525500174","year":"2025","publication_identifier":{"eissn":["1793-6314"],"issn":["0218-2025"]},"publication":"Mathematical Models and Methods in Applied Sciences","external_id":{"isi":["001456337300001"],"arxiv":["2411.01052"]},"date_published":"2025-05-01T00:00:00Z","abstract":[{"text":"Measuring distances in a multidimensional setting is a challenging problem, which appears in many fields of science and engineering. In this paper, to measure the distance between two multivariate distributions, we introduce a new measure of discrepancy which is scale invariant and which, in the case of two independent copies of the same distribution, and after normalization, coincides with the scaling invariant multidimensional version of the Gini index recently proposed in [P. Giudici, E. Raffinetti and G. Toscani, Measuring multidimensional inequality: A new proposal based on the Fourier transform, preprint (2024), arXiv:2401.14012 ]. A byproduct of the analysis is an easy-to-handle discrepancy metric, obtained by application of the theory to a pair of Gaussian multidimensional densities. The obtained metric does improve the standard metrics, based on the mean squared error, as it is scale invariant. The importance of this theoretical finding is illustrated by means of a real problem that concerns measuring the importance of Environmental, Social and Governance factors for the growth of small and medium enterprises. ","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.01052","open_access":"1"}],"issue":"5","author":[{"first_name":"Gennaro","full_name":"Auricchio, Gennaro","last_name":"Auricchio"},{"full_name":"Brigati, Giovanni","last_name":"Brigati","first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1"},{"first_name":"Paolo","full_name":"Giudici, Paolo","last_name":"Giudici"},{"full_name":"Toscani, Giuseppe","last_name":"Toscani","first_name":"Giuseppe"}],"day":"01","status":"public","_id":"19565","arxiv":1,"scopus_import":"1","department":[{"_id":"JaMa"}],"oa":1,"date_updated":"2025-09-30T11:36:56Z","month":"05","OA_place":"repository","intvolume":"        35","publisher":"World Scientific Publishing","volume":35,"OA_type":"green","quality_controlled":"1","citation":{"short":"G. Auricchio, G. Brigati, P. Giudici, G. Toscani, Mathematical Models and Methods in Applied Sciences 35 (2025) 1267–1296.","ista":"Auricchio G, Brigati G, Giudici P, Toscani G. 2025. Multivariate Gini-type discrepancies. Mathematical Models and Methods in Applied Sciences. 35(5), 1267–1296.","apa":"Auricchio, G., Brigati, G., Giudici, P., &#38; Toscani, G. (2025). Multivariate Gini-type discrepancies. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0218202525500174\">https://doi.org/10.1142/s0218202525500174</a>","mla":"Auricchio, Gennaro, et al. “Multivariate Gini-Type Discrepancies.” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 35, no. 5, World Scientific Publishing, 2025, pp. 1267–96, doi:<a href=\"https://doi.org/10.1142/s0218202525500174\">10.1142/s0218202525500174</a>.","ieee":"G. Auricchio, G. Brigati, P. Giudici, and G. Toscani, “Multivariate Gini-type discrepancies,” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 35, no. 5. World Scientific Publishing, pp. 1267–1296, 2025.","ama":"Auricchio G, Brigati G, Giudici P, Toscani G. Multivariate Gini-type discrepancies. <i>Mathematical Models and Methods in Applied Sciences</i>. 2025;35(5):1267-1296. doi:<a href=\"https://doi.org/10.1142/s0218202525500174\">10.1142/s0218202525500174</a>","chicago":"Auricchio, Gennaro, Giovanni Brigati, Paolo Giudici, and Giuseppe Toscani. “Multivariate Gini-Type Discrepancies.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing, 2025. <a href=\"https://doi.org/10.1142/s0218202525500174\">https://doi.org/10.1142/s0218202525500174</a>."},"page":"1267-1296","article_processing_charge":"No"},{"corr_author":"1","_id":"19566","status":"public","ddc":["570"],"file_date_updated":"2025-04-15T13:49:10Z","department":[{"_id":"SaSi"}],"scopus_import":"1","oa":1,"related_material":{"link":[{"url":"https://github.com/siegert-lab/RGC-Quant","relation":"software"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20467"}]},"date_updated":"2026-05-20T06:37:12Z","OA_place":"publisher","month":"03","publisher":"Association for Research in Vision and Ophthalmology","intvolume":"        66","has_accepted_license":"1","citation":{"apa":"Miteva, F. E., Maes, M. E., Alamalhoda, M., Firoozi, A., Colombo, G., &#38; Siegert, S. (2025). Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. <i>Investigative Ophthalmology &#38; Visual Science</i>. Association for Research in Vision and Ophthalmology. <a href=\"https://doi.org/10.1167/iovs.66.3.49\">https://doi.org/10.1167/iovs.66.3.49</a>","mla":"Miteva, Florianne E., et al. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” <i>Investigative Ophthalmology &#38; Visual Science</i>, vol. 66, no. 3, 49, Association for Research in Vision and Ophthalmology, 2025, doi:<a href=\"https://doi.org/10.1167/iovs.66.3.49\">10.1167/iovs.66.3.49</a>.","short":"F.E. Miteva, M.E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, S. Siegert, Investigative Ophthalmology &#38; Visual Science 66 (2025).","ista":"Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. 2025. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative Ophthalmology &#38; Visual Science. 66(3), 49.","chicago":"Miteva, Florianne E, Margaret E Maes, Mohammad Alamalhoda, Arsalan Firoozi, Gloria Colombo, and Sandra Siegert. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” <i>Investigative Ophthalmology &#38; Visual Science</i>. Association for Research in Vision and Ophthalmology, 2025. <a href=\"https://doi.org/10.1167/iovs.66.3.49\">https://doi.org/10.1167/iovs.66.3.49</a>.","ama":"Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. <i>Investigative Ophthalmology &#38; Visual Science</i>. 2025;66(3). doi:<a href=\"https://doi.org/10.1167/iovs.66.3.49\">10.1167/iovs.66.3.49</a>","ieee":"F. E. Miteva, M. E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, and S. Siegert, “Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye,” <i>Investigative Ophthalmology &#38; Visual Science</i>, vol. 66, no. 3. Association for Research in Vision and Ophthalmology, 2025."},"volume":66,"OA_type":"gold","quality_controlled":"1","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","DOAJ_listed":"1","publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"7be82147-9f16-11ee-852c-f44682d73140","name":"Dissecting the morpho-functional relationship of microglia","grant_number":"P37131"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"type":"journal_article","title":"Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye","date_created":"2025-04-15T13:40:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","publication_identifier":{"issn":["1552-5783"]},"article_number":"49","acknowledgement":"The authors thank the Scientific Service Units (SSU) of ISTA for the provided resources, specifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael Schunn, for mouse colony management and support. We thank all members of the Siegert group for constant feedback on the project and the manuscript. \r\nSupported in whole or in part by the Austrian Science Fund (FWF) [10.55776/P37131]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. ","doi":"10.1167/iovs.66.3.49","file":[{"checksum":"e8722ce5792f6c08fe1e191f7de6f147","access_level":"open_access","relation":"main_file","file_name":"2025_IOVS_SchootUiterkamp.pdf","file_id":"19567","date_updated":"2025-04-15T13:49:10Z","creator":"dernst","file_size":2721477,"success":1,"content_type":"application/pdf","date_created":"2025-04-15T13:49:10Z"}],"date_published":"2025-03-01T00:00:00Z","external_id":{"pmid":["40126507"]},"publication":"Investigative Ophthalmology & Visual Science","abstract":[{"text":"Purpose: Optic nerve crush (ONC) is a model for studying optic nerve trauma. Unilateral ONC induces massive retinal ganglion cell (RGC) degeneration in the affected eye, leading to vision loss within a month. A common assumption has been that the non-injured contralateral eye is unaffected due to the minimal retino-retinal projections of the RGCs at the chiasm. Yet, recently, microglia, the brain-resident macrophages, have shown a responsive phenotype in the contralateral eye after ONC. Whether RGC loss accompanies this phenotype is still controversial.\r\n\r\nMethods: Using the available RGCode algorithm and developing our own RGC-Quant deep-learning-based tool, we quantify RGC's total number and density across the entire retina after ONC.\r\n\r\nResults: We confirm a short-term microglia response in the contralateral eye after ONC, but this did not affect the microglia number. Furthermore, we cannot confirm the previously reported RGC loss between naïve and contralateral retinas 5 weeks after ONC induction across the commonly used Cx3cr1creERT2 and C57BL6/J mouse models. Neither sex nor the direct comparison of the RGC markers Brn3a and RBPMS, with Brn3a co-labeling, on average, 89% of the RBPMS+-cells, explained this discrepancy, suggesting that the early microglia-responsive phenotype does not have immediate consequences on the RGC number.\r\n\r\nConclusions: Our results corroborate that unilateral optic nerve injury elicits a microglial response in the uninjured contralateral eye but without RGC loss. Therefore, the contralateral eye should be treated separately and not as an ONC control.","lang":"eng"}],"issue":"3","pmid":1,"oa_version":"Published Version","APC_amount":"2236,02 EUR","day":"01","author":[{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E"},{"last_name":"Maes","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085"},{"first_name":"Mohammad","full_name":"Alamalhoda, Mohammad","last_name":"Alamalhoda"},{"last_name":"Firoozi","full_name":"Firoozi, Arsalan","first_name":"Arsalan"},{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Siegert","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","orcid":"0000-0001-8635-0877"}]},{"status":"public","_id":"19585","scopus_import":"1","department":[{"_id":"CaMu"}],"ddc":["550"],"date_updated":"2025-12-30T08:15:35Z","month":"07","intvolume":"       324","publisher":"Elsevier","quality_controlled":"1","volume":324,"OA_type":"closed access","citation":{"ama":"Antezana-Lopez F, Casallas Garcia A, Zhou G, et al. High-resolution anthropogenic emission inventories with deep learning in northern South America. <i>Remote Sensing of Environment</i>. 2025;324. doi:<a href=\"https://doi.org/10.1016/j.rse.2025.114761\">10.1016/j.rse.2025.114761</a>","chicago":"Antezana-Lopez, Franz, Alejandro Casallas Garcia, Guanhua Zhou, Kai Zhang, Guifei Jing, Aamir Ali, Ellie Lopez-Barrera, Luis Carlos Belalcazar, Nestor Rojas, and Hongzhi Jiang. “High-Resolution Anthropogenic Emission Inventories with Deep Learning in Northern South America.” <i>Remote Sensing of Environment</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rse.2025.114761\">https://doi.org/10.1016/j.rse.2025.114761</a>.","ieee":"F. Antezana-Lopez <i>et al.</i>, “High-resolution anthropogenic emission inventories with deep learning in northern South America,” <i>Remote Sensing of Environment</i>, vol. 324. Elsevier, 2025.","apa":"Antezana-Lopez, F., Casallas Garcia, A., Zhou, G., Zhang, K., Jing, G., Ali, A., … Jiang, H. (2025). High-resolution anthropogenic emission inventories with deep learning in northern South America. <i>Remote Sensing of Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rse.2025.114761\">https://doi.org/10.1016/j.rse.2025.114761</a>","mla":"Antezana-Lopez, Franz, et al. “High-Resolution Anthropogenic Emission Inventories with Deep Learning in Northern South America.” <i>Remote Sensing of Environment</i>, vol. 324, 114761, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rse.2025.114761\">10.1016/j.rse.2025.114761</a>.","short":"F. Antezana-Lopez, A. Casallas Garcia, G. Zhou, K. Zhang, G. Jing, A. Ali, E. Lopez-Barrera, L.C. Belalcazar, N. Rojas, H. Jiang, Remote Sensing of Environment 324 (2025).","ista":"Antezana-Lopez F, Casallas Garcia A, Zhou G, Zhang K, Jing G, Ali A, Lopez-Barrera E, Belalcazar LC, Rojas N, Jiang H. 2025. High-resolution anthropogenic emission inventories with deep learning in northern South America. Remote Sensing of Environment. 324, 114761."},"has_accepted_license":"1","article_processing_charge":"No","ec_funded":1,"publication_status":"published","article_type":"original","type":"journal_article","title":"High-resolution anthropogenic emission inventories with deep learning in northern South America","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-17T09:04:17Z","doi":"10.1016/j.rse.2025.114761","acknowledgement":"This project was supported by the National Natural Science Foundation of China (Grant No. 42471425). The research findings are a component of the SDGSAT-1 Open Science Program, which is conducted by the International Research Center of Big Data for Sustainable Development Goals (CBAS). The data utilized in this study is sourced from SDGSAT-1 and provided by CBAS. Alejandro Casallas was supported by a fellowship awarded by the Abdus Salam International Centre for Theoretical Physics and also by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Ellie López-Barrera was supported by project No. IN.BG.086.24.015 from Universidad Sergio Arboleda.","year":"2025","article_number":"114761","publication_identifier":{"eissn":["1879-0704"],"issn":["0034-4257"]},"publication":"Remote Sensing of Environment","date_published":"2025-07-01T00:00:00Z","external_id":{"isi":["001475174300001"]},"abstract":[{"lang":"eng","text":"Air quality in northern South America faces significant challenges due to insufficient high-resolution emission inventories and sparse atmospheric studies. This study addresses these gaps by developing a novel framework that integrates high-resolution nighttime light data from SDGSAT-1 and multisource remote sensing datasets with deep learning techniques to downscale emission inventories. The refined inventories are coupled with meteorological inputs into the Weather Research and Forecasting (WRF-Chem) model, enabling precise simulation of pollutant dynamics. Validated against ground measurements from Colombia's SISAIRE monitoring network, demonstrates significant improvements in spatiotemporal accuracy, particularly for particulate matter (PM) and nitrogen dioxide (NO₂) with error reductions of 22–30 % and correlation coefficients increasing from 0.68 to 0.85. These findings underscore the critical role of satellite-enhanced inventories in resolving localized emission patterns and seasonal variability, such as dry-season PM₁₀ spikes (150 % increase from wildfires). The framework provides policymakers with actionable insights to prioritize mitigation in rapidly urbanizing regions and manage transboundary pollution. By bridging data scarcity gaps, this replicable methodology offers transformative potential for global air quality management and public health protection, advocating for expanded ground monitoring networks and real-time satellite data integration in future applications."}],"oa_version":"None","author":[{"first_name":"Franz","full_name":"Antezana-Lopez, Franz","last_name":"Antezana-Lopez"},{"first_name":"Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","full_name":"Casallas Garcia, Alejandro","last_name":"Casallas Garcia","orcid":"0000-0002-1988-5035"},{"last_name":"Zhou","full_name":"Zhou, Guanhua","first_name":"Guanhua"},{"full_name":"Zhang, Kai","last_name":"Zhang","first_name":"Kai"},{"first_name":"Guifei","last_name":"Jing","full_name":"Jing, Guifei"},{"first_name":"Aamir","last_name":"Ali","full_name":"Ali, Aamir"},{"first_name":"Ellie","full_name":"Lopez-Barrera, Ellie","last_name":"Lopez-Barrera"},{"full_name":"Belalcazar, Luis Carlos","last_name":"Belalcazar","first_name":"Luis Carlos"},{"first_name":"Nestor","last_name":"Rojas","full_name":"Rojas, Nestor"},{"last_name":"Jiang","full_name":"Jiang, Hongzhi","first_name":"Hongzhi"}],"day":"01"},{"doi":"10.1186/s12974-025-03366-x","acknowledgement":"We thank the scientific service units at ISTA, specifically the Lab Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the Imaging and Optics Facility (IOF). We thank all members of the Siegert group and Marco Benevento for their constant feedback on the project and comments on the manuscript. A special thanks to Rouven Schulz for input on statistical analysis and sharing R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and Florianne Schoot Uiterkamp for their support in cell culture. This research was supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","article_number":"98","year":"2025","publication_identifier":{"eissn":["1742-2094"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","project":[{"name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"type":"journal_article","title":"Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids","isi":1,"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","DOAJ_listed":"1","author":[{"full_name":"Hübschmann, Verena","last_name":"Hübschmann","first_name":"Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4309-2251","full_name":"Korkut, Medina","last_name":"Korkut","first_name":"Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"id":"c815d433-1f5d-11f0-a875-dad18b1e5924","first_name":"Juan Pablo","last_name":"Maya-Arteaga","full_name":"Maya-Arteaga, Juan Pablo"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877"}],"day":"03","PlanS_conform":"1","APC_amount":"3948 EUR","oa_version":"Published Version","pmid":1,"issue":"1","abstract":[{"text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.","lang":"eng"}],"publication":"Journal of Neuroinflammation","file":[{"file_name":"2025_JourNeuroinflammation_Schmied.pdf","file_id":"19607","relation":"main_file","access_level":"open_access","checksum":"dcc355c21ab713e45fda5c61b5fa5299","success":1,"content_type":"application/pdf","date_created":"2025-04-22T09:46:27Z","file_size":4482167,"creator":"dernst","date_updated":"2025-04-22T09:46:27Z"}],"external_id":{"pmid":["40181459"],"isi":["001459311800002"]},"date_published":"2025-04-03T00:00:00Z","date_updated":"2026-05-06T12:49:37Z","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/pink-skies/","description":"News on ISTA website"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20074"}]},"oa":1,"scopus_import":"1","ddc":["570"],"department":[{"_id":"SaSi"}],"file_date_updated":"2025-04-22T09:46:27Z","status":"public","_id":"19593","corr_author":"1","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":22,"OA_type":"gold","quality_controlled":"1","has_accepted_license":"1","citation":{"ieee":"V. Schmied, M. Korkut, A. Venturino, J. P. Maya-Arteaga, and S. Siegert, “Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids,” <i>Journal of Neuroinflammation</i>, vol. 22, no. 1. Springer Nature, 2025.","chicago":"Schmied, Verena, Medina Korkut, Alessandro Venturino, Juan Pablo Maya-Arteaga, and Sandra Siegert. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” <i>Journal of Neuroinflammation</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s12974-025-03366-x\">https://doi.org/10.1186/s12974-025-03366-x</a>.","ama":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. <i>Journal of Neuroinflammation</i>. 2025;22(1). doi:<a href=\"https://doi.org/10.1186/s12974-025-03366-x\">10.1186/s12974-025-03366-x</a>","ista":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. 2025. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 22(1), 98.","short":"V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025).","mla":"Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” <i>Journal of Neuroinflammation</i>, vol. 22, no. 1, 98, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s12974-025-03366-x\">10.1186/s12974-025-03366-x</a>.","apa":"Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., &#38; Siegert, S. (2025). Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. <i>Journal of Neuroinflammation</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12974-025-03366-x\">https://doi.org/10.1186/s12974-025-03366-x</a>"},"intvolume":"        22","publisher":"Springer Nature","OA_place":"publisher","month":"04"},{"publisher":"Elsevier","intvolume":"        60","month":"04","article_processing_charge":"No","page":"1137-1139","citation":{"mla":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>, vol. 60, no. 8, Elsevier, 2025, pp. 1137–39, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>.","apa":"Benková, E. (2025). Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>","ista":"Benková E. 2025. Unlocking plant regeneration: The role for glutathione. Developmental Cell. 60(8), 1137–1139.","short":"E. Benková, Developmental Cell 60 (2025) 1137–1139.","ama":"Benková E. Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. 2025;60(8):1137-1139. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>","chicago":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>.","ieee":"E. Benková, “Unlocking plant regeneration: The role for glutathione,” <i>Developmental Cell</i>, vol. 60, no. 8. Elsevier, pp. 1137–1139, 2025."},"OA_type":"closed access","quality_controlled":"1","volume":60,"department":[{"_id":"EvBe"}],"scopus_import":"1","corr_author":"1","_id":"19594","status":"public","date_updated":"2025-09-30T12:07:36Z","abstract":[{"lang":"eng","text":"In this issue of Developmental Cell, Lee et al. identify a pivotal role for glutathione (GSH) in plant regeneration, a vital biological process enabling plants to regrow tissues and organs after injury. Applying single-cell RNA sequencing (scRNA-seq) and live imaging, the authors demonstrate that GSH, released upon tissue damage, accelerates cell-cycle transitions, particularly shortening the G1 phase, thereby facilitating efficient organ regeneration."}],"date_published":"2025-04-21T00:00:00Z","external_id":{"isi":["001477400800001"],"pmid":["40262524"]},"publication":"Developmental Cell","day":"21","author":[{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"issue":"8","pmid":1,"oa_version":"None","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"Unlocking plant regeneration: The role for glutathione","article_type":"letter_note","publication_status":"published","year":"2025","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"doi":"10.1016/j.devcel.2025.03.012","date_created":"2025-04-20T22:01:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"abstract":[{"text":"We investigate the locality of magnetic response in polycyclic aromatic molecules using a novel deep-learning approach. Our method employs graph neural networks (GNNs) with a graph-of-rings representation to predict nucleus independent chemical shifts (NICS) in the space around the molecule. We train a series of models, each time reducing the size of the largest molecules used in training. The accuracy of prediction remains high (MAE < 0.5 ppm), even when training the model only on molecules with up to four rings, thus providing strong evidence for the locality of magnetic response. To overcome the known problem of generalization of GNNs, we implement a k-hop expansion strategy and succeed in achieving accurate predictions for molecules with up to 15 rings (almost 4 times the size of the largest training example). Our findings have implications for understanding the magnetic response in complex molecules and demonstrate a promising approach to overcoming GNN scalability limitations. Furthermore, the trained models enable rapid characterization, without the need for more expensive DFT calculations.","lang":"eng"}],"publication":"Journal of Chemical Physics","file":[{"checksum":"20a31a4c506b52de863bab7d3ff989ef","file_id":"19606","file_name":"2025_JourChemicalPhysics_Davidson.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2025-04-22T09:27:43Z","date_created":"2025-04-22T09:27:43Z","content_type":"application/pdf","success":1,"file_size":7812182}],"external_id":{"pmid":["40197568"],"isi":["001466311300030"]},"date_published":"2025-04-14T00:00:00Z","author":[{"first_name":"Yair","last_name":"Davidson","full_name":"Davidson, Yair"},{"full_name":"Philipp, Aviad","last_name":"Philipp","first_name":"Aviad"},{"first_name":"Sabyasachi","last_name":"Chakraborty","full_name":"Chakraborty, Sabyasachi"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"},{"full_name":"Gershoni-Poranne, Renana","last_name":"Gershoni-Poranne","first_name":"Renana"}],"day":"14","oa_version":"Published Version","pmid":1,"issue":"14","project":[{"_id":"92f4a086-16d5-11f0-9cad-c929f5c58b0c","grant_number":"863839","name":"Acoustics-based drone navigation and interaction"}],"type":"journal_article","title":"How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons","language":[{"iso":"eng"}],"isi":1,"publication_status":"published","article_type":"original","acknowledgement":"The authors express their gratitude to Professor Dr. Peter Chen for his continued support. The authors acknowledge the Branco Weiss Fellowship for supporting this research as part of a Society in Science grant and the Israel Science Foundation for financial support (Grant No. 1745/23 to R.G.-P.). R.G.-P. is a Branco Weiss Fellow, a Horev Fellow, and an Alon Scholarship recipient. A.M.B. was supported by the ERC StG EARS and the Israeli Science Foundation.","doi":"10.1063/5.0257558","article_number":"144101","year":"2025","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2025-04-20T22:01:28Z","intvolume":"       162","publisher":"AIP Publishing","OA_place":"publisher","month":"04","article_processing_charge":"Yes (in subscription journal)","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"OA_type":"hybrid","quality_controlled":"1","volume":162,"has_accepted_license":"1","citation":{"ieee":"Y. Davidson, A. Philipp, S. Chakraborty, A. M. Bronstein, and R. Gershoni-Poranne, “How local is ‘local’? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons,” <i>Journal of Chemical Physics</i>, vol. 162, no. 14. AIP Publishing, 2025.","chicago":"Davidson, Yair, Aviad Philipp, Sabyasachi Chakraborty, Alex M. Bronstein, and Renana Gershoni-Poranne. “How Local Is ‘Local’? Deep Learning Reveals Locality of the Induced Magnetic Field of Polycyclic Aromatic Hydrocarbons.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0257558\">https://doi.org/10.1063/5.0257558</a>.","ama":"Davidson Y, Philipp A, Chakraborty S, Bronstein AM, Gershoni-Poranne R. How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. <i>Journal of Chemical Physics</i>. 2025;162(14). doi:<a href=\"https://doi.org/10.1063/5.0257558\">10.1063/5.0257558</a>","ista":"Davidson Y, Philipp A, Chakraborty S, Bronstein AM, Gershoni-Poranne R. 2025. How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. Journal of Chemical Physics. 162(14), 144101.","short":"Y. Davidson, A. Philipp, S. Chakraborty, A.M. Bronstein, R. Gershoni-Poranne, Journal of Chemical Physics 162 (2025).","apa":"Davidson, Y., Philipp, A., Chakraborty, S., Bronstein, A. M., &#38; Gershoni-Poranne, R. (2025). How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0257558\">https://doi.org/10.1063/5.0257558</a>","mla":"Davidson, Yair, et al. “How Local Is ‘Local’? Deep Learning Reveals Locality of the Induced Magnetic Field of Polycyclic Aromatic Hydrocarbons.” <i>Journal of Chemical Physics</i>, vol. 162, no. 14, 144101, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0257558\">10.1063/5.0257558</a>."},"scopus_import":"1","ddc":["000"],"department":[{"_id":"AlBr"}],"file_date_updated":"2025-04-22T09:27:43Z","status":"public","corr_author":"1","_id":"19595","date_updated":"2025-09-30T12:06:51Z","related_material":{"link":[{"url":"https://gitlab.com/porannegroup/magnetic_locality","relation":"software"}]},"oa":1},{"oa":1,"date_updated":"2026-02-16T12:42:28Z","_id":"19596","status":"public","ddc":["520"],"department":[{"_id":"JoMa"}],"file_date_updated":"2025-04-22T09:08:17Z","arxiv":1,"scopus_import":"1","has_accepted_license":"1","citation":{"ieee":"A. Weibel <i>et al.</i>, “RUBIES reveals a massive quiescent galaxy at z = 7.3,” <i>The Astrophysical Journal</i>, vol. 983, no. 1. IOP Publishing, 2025.","ama":"Weibel A, De Graaff A, Setton DJ, et al. RUBIES reveals a massive quiescent galaxy at z = 7.3. <i>The Astrophysical Journal</i>. 2025;983(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/adab7a\">10.3847/1538-4357/adab7a</a>","chicago":"Weibel, Andrea, Anna De Graaff, David J. Setton, Tim B. Miller, Pascal A. Oesch, Gabriel Brammer, Claudia D.P. Lagos, et al. “RUBIES Reveals a Massive Quiescent Galaxy at z = 7.3.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/adab7a\">https://doi.org/10.3847/1538-4357/adab7a</a>.","short":"A. Weibel, A. De Graaff, D.J. Setton, T.B. Miller, P.A. Oesch, G. Brammer, C.D.P. Lagos, K.E. Whitaker, C.C. Williams, J.F.W. Baggen, R. Bezanson, L.A. Boogaard, N.J. Cleri, J.E. Greene, M. Hirschmann, R.E. Hviding, A. Kuruvanthodi, I. Labbé, J. Leja, M.V. Maseda, J.J. Matthee, I. Mcconachie, R.P. Naidu, G. Roberts-Borsani, D. Schaerer, K.A. Suess, F. Valentino, P. Van Dokkum, B. Wang, The Astrophysical Journal 983 (2025).","ista":"Weibel A, De Graaff A, Setton DJ, Miller TB, Oesch PA, Brammer G, Lagos CDP, Whitaker KE, Williams CC, Baggen JFW, Bezanson R, Boogaard LA, Cleri NJ, Greene JE, Hirschmann M, Hviding RE, Kuruvanthodi A, Labbé I, Leja J, Maseda MV, Matthee JJ, Mcconachie I, Naidu RP, Roberts-Borsani G, Schaerer D, Suess KA, Valentino F, Van Dokkum P, Wang B. 2025. RUBIES reveals a massive quiescent galaxy at z = 7.3. The Astrophysical Journal. 983(1), 11.","apa":"Weibel, A., De Graaff, A., Setton, D. J., Miller, T. B., Oesch, P. A., Brammer, G., … Wang, B. (2025). RUBIES reveals a massive quiescent galaxy at z = 7.3. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/adab7a\">https://doi.org/10.3847/1538-4357/adab7a</a>","mla":"Weibel, Andrea, et al. “RUBIES Reveals a Massive Quiescent Galaxy at z = 7.3.” <i>The Astrophysical Journal</i>, vol. 983, no. 1, 11, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/adab7a\">10.3847/1538-4357/adab7a</a>."},"quality_controlled":"1","OA_type":"gold","volume":983,"article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"04","publisher":"IOP Publishing","intvolume":"       983","date_created":"2025-04-20T22:01:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"11","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"year":"2025","doi":"10.3847/1538-4357/adab7a","acknowledgement":"We thank the PRIMER team 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 program #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. 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 (DNRF140). 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 was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. Support for this work for R.P.N. 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. T.B.M. was supported by a CIERA fellowship.\r\nAll software packages used in this work are publicly available on Github: grizli, msafit, msaexp, Prospector, and sedpy. We acknowledge: astropy (Astropy Collaboration et al. 2013, 2018, 2022), matplotlib (J. D. Hunter 2007), numpy (C. R. Harris et al. 2020), scipy (P. Virtanen et al. 2020), lmfit (M. Newville et al. 2024), eMPT (N. Bonaventura et al. 2023), the jwst pipeline (H. Bushouse et al. 2024), msaexp (G. Brammer 2024a), and grizli (G. Brammer 2024b),.","article_type":"original","DOAJ_listed":"1","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"RUBIES reveals a massive quiescent galaxy at z = 7.3","issue":"1","oa_version":"Published Version","day":"10","author":[{"last_name":"Weibel","full_name":"Weibel, Andrea","first_name":"Andrea"},{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"last_name":"Setton","full_name":"Setton, David J.","first_name":"David J."},{"first_name":"Tim B.","last_name":"Miller","full_name":"Miller, Tim B."},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"full_name":"Lagos, Claudia D.P.","last_name":"Lagos","first_name":"Claudia D.P."},{"last_name":"Whitaker","full_name":"Whitaker, Katherine E.","first_name":"Katherine E."},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."},{"full_name":"Baggen, Josephine F.W.","last_name":"Baggen","first_name":"Josephine F.W."},{"last_name":"Bezanson","full_name":"Bezanson, Rachel","first_name":"Rachel"},{"full_name":"Boogaard, Leindert A.","last_name":"Boogaard","first_name":"Leindert A."},{"first_name":"Nikko J.","full_name":"Cleri, Nikko J.","last_name":"Cleri"},{"first_name":"Jenny E.","last_name":"Greene","full_name":"Greene, Jenny E."},{"full_name":"Hirschmann, Michaela","last_name":"Hirschmann","first_name":"Michaela"},{"first_name":"Raphael E.","full_name":"Hviding, Raphael E.","last_name":"Hviding"},{"first_name":"Adarsh","full_name":"Kuruvanthodi, Adarsh","last_name":"Kuruvanthodi"},{"first_name":"Ivo","full_name":"Labbé, Ivo","last_name":"Labbé"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"first_name":"Michael V.","full_name":"Maseda, Michael V.","last_name":"Maseda"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X"},{"first_name":"Ian","full_name":"Mcconachie, Ian","last_name":"Mcconachie"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"first_name":"Guido","last_name":"Roberts-Borsani","full_name":"Roberts-Borsani, Guido"},{"first_name":"Daniel","last_name":"Schaerer","full_name":"Schaerer, Daniel"},{"last_name":"Suess","full_name":"Suess, Katherine A.","first_name":"Katherine A."},{"full_name":"Valentino, Francesco","last_name":"Valentino","first_name":"Francesco"},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"first_name":"Bingjie","last_name":"Wang","full_name":"Wang, Bingjie"}],"file":[{"access_level":"open_access","relation":"main_file","file_name":"2025_AstrophysicalJour_Weibel.pdf","file_id":"19605","checksum":"a1132e0b18bb643f9a32674c6694375a","file_size":1964589,"success":1,"date_created":"2025-04-22T09:08:17Z","content_type":"application/pdf","date_updated":"2025-04-22T09:08:17Z","creator":"dernst"}],"external_id":{"arxiv":["2409.03829"],"isi":["001457334900001"]},"date_published":"2025-04-10T00:00:00Z","publication":"The Astrophysical Journal","abstract":[{"lang":"eng","text":"We report the spectroscopic discovery of a massive quiescent galaxy at zspec = 7.29 ± 0.01, just ∼700 Myr after the big bang. RUBIES-UDS-QG-z7 was selected from public JWST/NIRCam and MIRI imaging from the PRIMER survey and observed with JWST/NIRSpec as part of RUBIES. The NIRSpec/PRISM spectrum reveals one of the strongest Balmer breaks observed thus far at z > 6, with no emission lines but tentative Balmer and Ca absorption features, as well as a Lyman break. Simultaneous modeling of the NIRSpec/PRISM spectrum and NIRCam and MIRI photometry (spanning 0.9–18 μm) shows that the galaxy formed a stellar mass of\r\n(math. formular) before z ∼ 8 and ceased forming stars 50–100 Myr prior to the time of observation, resulting in log (sSFR/Gyr- 1) < -1 . We measure a small physical size of (math formular) , which implies a high stellarmass surface density within the effective radius of (math formular) comparable to the highest densities measured in quiescent galaxies at z ∼ 2–5. The 3D stellar-mass density profile of RUBIES-UDS-QG-z7 is remarkably similar to the central densities of local massive ellipticals, suggesting that at least some of their cores may have already been in place at z > 7. The discovery of RUBIES-UDS-QG-z7 has strong implications for galaxy formation models: the estimated number density of quiescent galaxies at z ∼ 7 is >100 × larger than predicted from any model to date, indicating that quiescent galaxies have formed earlier than previously expected. "}]},{"publication_status":"published","DOAJ_listed":"1","article_type":"original","title":"Subgap transport in superconductor-semiconductor hybrid islands: Weak and strong coupling regimes","type":"journal_article","project":[{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","doi":"10.1103/PhysRevResearch.7.023022","acknowledgement":"This research was supported by the Scientific Service Units of ISTA, through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the FWF Project with DOI10.55776/F86. We acknowledge support from the European Research Council under the European Unions Horizon 2020 research and innovation programme under Grant Agreement No. 856526, the Swedish Research Council under Grant Agreement No. 2020-03412, the Spanish Comunidad de Madrid (CM) “Talento Program” (Project No. 2022-T1/IND-24070), the Spanish Ministry of Science, innovation, and Universities through Grant PID2022-140552NA-I00 and NanoLund.","year":"2025","article_number":"023022","publication_identifier":{"issn":["2643-1564"]},"publication":"Physical Review Research","file":[{"file_name":"2025_PhysReviewResearch_Valentini.pdf","file_id":"19604","access_level":"open_access","relation":"main_file","checksum":"535351066e9c900340ef014893a09ac8","success":1,"content_type":"application/pdf","date_created":"2025-04-22T09:00:08Z","file_size":1977581,"creator":"dernst","date_updated":"2025-04-22T09:00:08Z"}],"date_published":"2025-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"Superconductor–semiconductor hybrid systems play a crucial role in realizing nanoscale quantum devices, including hybrid qubits, Majorana bound states, and Kitaev chains. For such hybrid devices, subgap states play a prominent role in their operation. In this paper, we study these subgap states via Coulomb and tunneling spectroscopy through a superconducting island defined in a semiconductor nanowire fully coated by a superconductor. We systematically explore regimes ranging from an almost decoupled island to the open configuration. In the weak-coupling regime, the experimental observations are very similar in the absence of a magnetic field and when one flux quantum pierces the superconducting shell. Conversely, in the strong-coupling regime, significant distinctions emerge between the two cases. We attribute this distinct behavior to the existence of subgap states at one flux quantum, which become observable only for sufficiently strong coupling to the leads. We support our interpretation using a simple model to describe transport through the island. Our study highlights the importance of studying a broad range of tunnel couplings for understanding the rich physics of hybrid devices."}],"oa_version":"Published Version","issue":"2","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"first_name":"Rubén Seoane","last_name":"Souto","full_name":"Souto, Rubén Seoane"},{"full_name":"Borovkov, Maksim","last_name":"Borovkov","first_name":"Maksim","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5"},{"full_name":"Krogstrup, Peter","last_name":"Krogstrup","first_name":"Peter"},{"first_name":"Yigal","full_name":"Meir, Yigal","last_name":"Meir"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"PlanS_conform":"1","day":"01","APC_amount":"3036,92 EUR","status":"public","corr_author":"1","_id":"19597","scopus_import":"1","department":[{"_id":"GeKa"}],"file_date_updated":"2025-04-22T09:00:08Z","ddc":["530"],"oa":1,"date_updated":"2026-06-11T09:13:12Z","month":"04","OA_place":"publisher","intvolume":"         7","publisher":"American Physical Society","volume":7,"quality_controlled":"1","OA_type":"hybrid","citation":{"ista":"Valentini M, Souto RS, Borovkov M, Krogstrup P, Meir Y, Leijnse M, Danon J, Katsaros G. 2025. Subgap transport in superconductor-semiconductor hybrid islands: Weak and strong coupling regimes. Physical Review Research. 7(2), 023022.","short":"M. Valentini, R.S. Souto, M. Borovkov, P. Krogstrup, Y. Meir, M. Leijnse, J. Danon, G. Katsaros, Physical Review Research 7 (2025).","apa":"Valentini, M., Souto, R. S., Borovkov, M., Krogstrup, P., Meir, Y., Leijnse, M., … Katsaros, G. (2025). Subgap transport in superconductor-semiconductor hybrid islands: Weak and strong coupling regimes. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.7.023022\">https://doi.org/10.1103/PhysRevResearch.7.023022</a>","mla":"Valentini, Marco, et al. “Subgap Transport in Superconductor-Semiconductor Hybrid Islands: Weak and Strong Coupling Regimes.” <i>Physical Review Research</i>, vol. 7, no. 2, 023022, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.7.023022\">10.1103/PhysRevResearch.7.023022</a>.","ieee":"M. Valentini <i>et al.</i>, “Subgap transport in superconductor-semiconductor hybrid islands: Weak and strong coupling regimes,” <i>Physical Review Research</i>, vol. 7, no. 2. American Physical Society, 2025.","chicago":"Valentini, Marco, Rubén Seoane Souto, Maksim Borovkov, Peter Krogstrup, Yigal Meir, Martin Leijnse, Jeroen Danon, and Georgios Katsaros. “Subgap Transport in Superconductor-Semiconductor Hybrid Islands: Weak and Strong Coupling Regimes.” <i>Physical Review Research</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevResearch.7.023022\">https://doi.org/10.1103/PhysRevResearch.7.023022</a>.","ama":"Valentini M, Souto RS, Borovkov M, et al. Subgap transport in superconductor-semiconductor hybrid islands: Weak and strong coupling regimes. <i>Physical Review Research</i>. 2025;7(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.7.023022\">10.1103/PhysRevResearch.7.023022</a>"},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"Yes"},{"date_updated":"2026-04-07T12:32:19Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20575"}]},"oa":1,"arxiv":1,"scopus_import":"1","department":[{"_id":"LaEr"}],"file_date_updated":"2025-12-30T13:10:05Z","ddc":["510"],"status":"public","_id":"19598","corr_author":"1","page":"1183-1237","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","volume":193,"quality_controlled":"1","citation":{"ieee":"V. Riabov, “Linear Eigenvalue statistics at the cusp,” <i>Probability Theory and Related Fields</i>, vol. 193. Springer Nature, pp. 1183–1237, 2025.","chicago":"Riabov, Volodymyr. “Linear Eigenvalue Statistics at the Cusp.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00440-025-01373-w\">https://doi.org/10.1007/s00440-025-01373-w</a>.","ama":"Riabov V. Linear Eigenvalue statistics at the cusp. <i>Probability Theory and Related Fields</i>. 2025;193:1183-1237. doi:<a href=\"https://doi.org/10.1007/s00440-025-01373-w\">10.1007/s00440-025-01373-w</a>","short":"V. Riabov, Probability Theory and Related Fields 193 (2025) 1183–1237.","ista":"Riabov V. 2025. Linear Eigenvalue statistics at the cusp. Probability Theory and Related Fields. 193, 1183–1237.","apa":"Riabov, V. (2025). Linear Eigenvalue statistics at the cusp. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-025-01373-w\">https://doi.org/10.1007/s00440-025-01373-w</a>","mla":"Riabov, Volodymyr. “Linear Eigenvalue Statistics at the Cusp.” <i>Probability Theory and Related Fields</i>, vol. 193, Springer Nature, 2025, pp. 1183–237, doi:<a href=\"https://doi.org/10.1007/s00440-025-01373-w\">10.1007/s00440-025-01373-w</a>."},"has_accepted_license":"1","intvolume":"       193","publisher":"Springer Nature","month":"12","OA_place":"publisher","acknowledgement":"I would like to express my gratitude to László Erdős for his careful guidance and supervision of my work. I am also thankful to Jana Reker and Joscha Henheik for many helpful discussions. Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s00440-025-01373-w","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","type":"journal_article","title":"Linear Eigenvalue statistics at the cusp","isi":1,"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","author":[{"last_name":"Riabov","full_name":"Riabov, Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","first_name":"Volodymyr"}],"PlanS_conform":"1","day":"01","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We establish universal Gaussian fluctuations for the mesoscopic linear eigenvalue statistics in the vicinity of the cusp-like singularities of the limiting spectral density for Wigner-type random matrices. Prior to this work, the linear eigenvalue statistics at the cusp-like singularities were not studied in any ensemble. Our analysis covers not only the exact cusps but the entire transitionary regime from the square-root singularity at a regular edge through the sharp cusp to the bulk. We identify a new one-parameter family of functionals that govern the limiting bias and variance, continuously interpolating between the previously known formulas in the bulk and at a regular edge. Since cusps are the only possible singularities besides the regular edges, our result gives a complete description of the linear eigenvalue statistics in all regimes."}],"publication":"Probability Theory and Related Fields","date_published":"2025-12-01T00:00:00Z","file":[{"file_name":"2025_ProbTheoryRelatFields_Riabov.pdf","file_id":"20916","access_level":"open_access","relation":"main_file","checksum":"700229b280725c0d6aad0d71362cce5f","success":1,"date_created":"2025-12-30T13:10:05Z","content_type":"application/pdf","file_size":919213,"creator":"dernst","date_updated":"2025-12-30T13:10:05Z"}],"external_id":{"arxiv":["2307.07432"],"isi":["001466997300001"]}},{"status":"public","_id":"19599","corr_author":"1","scopus_import":"1","file_date_updated":"2025-08-05T13:04:42Z","department":[{"_id":"BaPi"}],"ddc":["540"],"oa":1,"date_updated":"2025-10-02T08:22:12Z","month":"04","OA_place":"publisher","intvolume":"       147","publisher":"American Chemical Society","OA_type":"hybrid","volume":147,"quality_controlled":"1","citation":{"apa":"Anghileri, L., Baunis, H., Bena, A., Giannoudis, C., Burke, J. H., Reischauer, S., … Pieber, B. (2025). Evidence for a unifying NiI/NiIII mechanism in light-mediated cross-coupling catalysis. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.4c16050\">https://doi.org/10.1021/jacs.4c16050</a>","mla":"Anghileri, Lucia, et al. “Evidence for a Unifying NiI/NiIII Mechanism in Light-Mediated Cross-Coupling Catalysis.” <i>Journal of the American Chemical Society</i>, vol. 147, no. 16, American Chemical Society, 2025, pp. 13169–13179, doi:<a href=\"https://doi.org/10.1021/jacs.4c16050\">10.1021/jacs.4c16050</a>.","short":"L. Anghileri, H. Baunis, A. Bena, C. Giannoudis, J.H. Burke, S. Reischauer, C. Merschjann, R.F. Wallick, T. Al Said, C.E. Adams, G. Simionato, S. Kovalenko, L. Dell’Amico, R.M. Van Der Veen, B. Pieber, Journal of the American Chemical Society 147 (2025) 13169–13179.","ista":"Anghileri L, Baunis H, Bena A, Giannoudis C, Burke JH, Reischauer S, Merschjann C, Wallick RF, Al Said T, Adams CE, Simionato G, Kovalenko S, Dell’Amico L, Van Der Veen RM, Pieber B. 2025. Evidence for a unifying NiI/NiIII mechanism in light-mediated cross-coupling catalysis. Journal of the American Chemical Society. 147(16), 13169–13179.","chicago":"Anghileri, Lucia, Haralds Baunis, Aleksander Bena, Christos Giannoudis, John H. Burke, Susanne Reischauer, Christoph Merschjann, et al. “Evidence for a Unifying NiI/NiIII Mechanism in Light-Mediated Cross-Coupling Catalysis.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/jacs.4c16050\">https://doi.org/10.1021/jacs.4c16050</a>.","ama":"Anghileri L, Baunis H, Bena A, et al. Evidence for a unifying NiI/NiIII mechanism in light-mediated cross-coupling catalysis. <i>Journal of the American Chemical Society</i>. 2025;147(16):13169–13179. doi:<a href=\"https://doi.org/10.1021/jacs.4c16050\">10.1021/jacs.4c16050</a>","ieee":"L. Anghileri <i>et al.</i>, “Evidence for a unifying NiI/NiIII mechanism in light-mediated cross-coupling catalysis,” <i>Journal of the American Chemical Society</i>, vol. 147, no. 16. American Chemical Society, pp. 13169–13179, 2025."},"has_accepted_license":"1","page":"13169–13179","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"NMR"}],"publication_status":"published","article_type":"original","type":"journal_article","title":"Evidence for a unifying NiI/NiIII mechanism in light-mediated cross-coupling catalysis","project":[{"_id":"8f1d607d-16d5-11f0-9cad-ab453295ba5e","grant_number":"PAT 1250924","name":"Photoactive ligands for transformative nickel catalysis"}],"language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Lab Support Facility (LSF), Mass Spec Facility, and NMR Facility. We gratefully acknowledge the Institute of Science and Technology Austria (ISTA) and the Max-Planck Society for their generous financial support. R.M.v.d.V. and B.P. thank the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2008 – 390540038 – UniSysCat for funding. B.P. thanks the DFG (PI 1635/2-19), the Boehringer Ingelheim Foundation (Plus 3 Perspectives Programme), and the FWF (Austrian Science Fund; PAT 1250924) for financial support. J.H.B. acknowledges the Robert C. and Carolyn J. Springborn Endowment for Student Support Program at the University of Illinois Urbana–Champaign. R.F.W. was supported by a fellowship from the Deutscher Akademischer Austauschdienst (DAAD). We thank Dr. John J. Molloy (MPICI) for scientific discussions.","doi":"10.1021/jacs.4c16050","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"year":"2025","publication":"Journal of the American Chemical Society","file":[{"checksum":"7f2b6a3c23b062490f37cce10ced46aa","relation":"main_file","access_level":"open_access","file_name":"2025_JACS_Anghileri.pdf","file_id":"20137","date_updated":"2025-08-05T13:04:42Z","creator":"dernst","file_size":4179314,"success":1,"content_type":"application/pdf","date_created":"2025-08-05T13:04:42Z"}],"date_published":"2025-04-11T00:00:00Z","external_id":{"isi":["001465858000001"],"pmid":["40211781"]},"abstract":[{"text":"Advances in nickel catalysis have significantly broadened the synthetic chemists’ toolbox, particularly through methodologies leveraging paramagnetic nickel species via photoredox catalysis or electrochemistry. Key to these reactions is the oxidation state modulation of nickel via single-electron transfer events. Recent mechanistic studies indicate that C(sp2)–heteroatom bond formations proceed through NiI/NiIII cycles. Related C(sp2)–C(sp3) cross-couplings operate via the photocatalytic generation of C-centered radicals and a catalytic cycle that involves Ni0, NiI, and NiIII species. Here, we show that light-mediated nickel-catalyzed C(sp2)–C(sp3) bond formations can be carried out without using exogenous photoredox catalysts but with a photoactive ligand. In a pursuit of expanding the scope of C(sp2)–heteroatom couplings using donor–acceptor ligands, we identified a photoactive nickel complex capable of catalyzing cross-couplings between aryl halides and benzyltrifluoroborate salts. Mechanistic investigations provide evidence that transmetalation between a photochemically generated NiI species and the organoboron compound is the key catalytic step in a NiI/NiIII catalytic cycle under these conditions.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"16","author":[{"last_name":"Anghileri","full_name":"Anghileri, Lucia","id":"7b65e46e-1f51-11f0-8ea0-faa153157f5e","first_name":"Lucia"},{"first_name":"Haralds","id":"2eea55ec-e8ec-11ed-86cb-d9c76787acfe","full_name":"Baunis, Haralds","last_name":"Baunis"},{"full_name":"Bena, Aleksander","last_name":"Bena","first_name":"Aleksander","id":"4197c39e-e8ec-11ed-86cb-afed934cd664"},{"last_name":"Giannoudis","full_name":"Giannoudis, Christos","id":"1bd506c6-e8ec-11ed-86cb-d495f63f2dcd","first_name":"Christos"},{"first_name":"John H.","full_name":"Burke, John H.","last_name":"Burke"},{"last_name":"Reischauer","full_name":"Reischauer, Susanne","first_name":"Susanne"},{"full_name":"Merschjann, Christoph","last_name":"Merschjann","first_name":"Christoph"},{"first_name":"Rachel F.","last_name":"Wallick","full_name":"Wallick, Rachel F."},{"first_name":"Tarek","last_name":"Al Said","full_name":"Al Said, Tarek"},{"first_name":"Callum E","id":"126d6d0f-fdc1-11ee-bb4a-9f462709fa9d","full_name":"Adams, Callum E","last_name":"Adams"},{"first_name":"Gianluca","last_name":"Simionato","full_name":"Simionato, Gianluca"},{"full_name":"Kovalenko, Sergey","last_name":"Kovalenko","first_name":"Sergey"},{"last_name":"Dell’Amico","full_name":"Dell’Amico, Luca","first_name":"Luca"},{"first_name":"Renske M.","full_name":"Van Der Veen, Renske M.","last_name":"Van Der Veen"},{"orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus","last_name":"Pieber"}],"PlanS_conform":"1","day":"11"},{"OA_type":"green","volume":15263,"quality_controlled":"1","citation":{"ieee":"Z. Avarikioti, M. Bastankhah, M. A. Maddah-Ali, K. Z. Pietrzak, J. Svoboda, and M. X. Yeo, “Route discovery in private payment channel networks,” in <i>Computer Security. ESORICS 2024 International Workshops</i>, Bydgoszcz, Poland, 2025, vol. 15263, pp. 207–223.","chicago":"Avarikioti, Zeta, Mahsa Bastankhah, Mohammad Ali Maddah-Ali, Krzysztof Z Pietrzak, Jakub Svoboda, and Michelle X Yeo. “Route Discovery in Private Payment Channel Networks.” In <i>Computer Security. ESORICS 2024 International Workshops</i>, 15263:207–23. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-031-82349-7_15\">https://doi.org/10.1007/978-3-031-82349-7_15</a>.","ama":"Avarikioti Z, Bastankhah M, Maddah-Ali MA, Pietrzak KZ, Svoboda J, Yeo MX. Route discovery in private payment channel networks. In: <i>Computer Security. ESORICS 2024 International Workshops</i>. Vol 15263. Springer Nature; 2025:207-223. doi:<a href=\"https://doi.org/10.1007/978-3-031-82349-7_15\">10.1007/978-3-031-82349-7_15</a>","short":"Z. Avarikioti, M. Bastankhah, M.A. Maddah-Ali, K.Z. Pietrzak, J. Svoboda, M.X. Yeo, in:, Computer Security. ESORICS 2024 International Workshops, Springer Nature, 2025, pp. 207–223.","ista":"Avarikioti Z, Bastankhah M, Maddah-Ali MA, Pietrzak KZ, Svoboda J, Yeo MX. 2025. Route discovery in private payment channel networks. Computer Security. ESORICS 2024 International Workshops. ESORICS: European Symposium on Research in Computer Security, LNCS, vol. 15263, 207–223.","apa":"Avarikioti, Z., Bastankhah, M., Maddah-Ali, M. A., Pietrzak, K. Z., Svoboda, J., &#38; Yeo, M. X. (2025). Route discovery in private payment channel networks. In <i>Computer Security. ESORICS 2024 International Workshops</i> (Vol. 15263, pp. 207–223). Bydgoszcz, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-82349-7_15\">https://doi.org/10.1007/978-3-031-82349-7_15</a>","mla":"Avarikioti, Zeta, et al. “Route Discovery in Private Payment Channel Networks.” <i>Computer Security. ESORICS 2024 International Workshops</i>, vol. 15263, Springer Nature, 2025, pp. 207–23, doi:<a href=\"https://doi.org/10.1007/978-3-031-82349-7_15\">10.1007/978-3-031-82349-7_15</a>."},"page":"207-223","ec_funded":1,"article_processing_charge":"No","month":"04","OA_place":"repository","intvolume":"     15263","publisher":"Springer Nature","oa":1,"date_updated":"2025-11-05T07:52:35Z","status":"public","_id":"19600","scopus_import":"1","department":[{"_id":"KrPi"},{"_id":"KrCh"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://eprint.iacr.org/2021/1539","open_access":"1"}],"author":[{"first_name":"Zeta","last_name":"Avarikioti","full_name":"Avarikioti, Zeta"},{"first_name":"Mahsa","full_name":"Bastankhah, Mahsa","last_name":"Bastankhah"},{"first_name":"Mohammad Ali","full_name":"Maddah-Ali, Mohammad Ali","last_name":"Maddah-Ali"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"orcid":"0000-0002-1419-3267","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","last_name":"Svoboda"},{"orcid":"0009-0001-3676-4809","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo"}],"day":"01","publication":"Computer Security. ESORICS 2024 International Workshops","date_published":"2025-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"In this work, we explore route discovery in private payment channel networks. We first determine what “ideal\" privacy for a routing protocol means in this setting. We observe that protocols achieving this strong privacy definition exist by leveraging Multi-Party Computation but they are inherently inefficient as they must involve the entire network. We then present protocols with weaker privacy guarantees but much better efficiency (involving only a small fraction of the nodes). The core idea is that both sender and receiver gossip a message which propagates through the network, and the moment any node in the network receives both messages, a path is found. In our first protocol the message is always sent to all neighbouring nodes with a delay proportional to the fees of that edge. In our second protocol the message is only sent to one neighbour chosen randomly with a probability proportional to its degree. We additionally propose a more realistic notion of privacy in order to measure the privacy leakage of our protocols in practice. Our realistic notion of privacy challenges an adversary that join the network with a fixed budget to create channels to guess the sender and receiver of a transaction upon receiving messages from our protocols. Simulations of our protocols on the Lightning network topology (for random transactions and uniform fees) show that 1) forming edges with high degree nodes is a more effective attack strategy for the adversary, 2) there is a tradeoff between the number of nodes involved in our protocols (privacy) and the optimality of the discovered path, and 3) our protocols involve a very small fraction of the network on average."}],"conference":{"end_date":"2024-09-20","location":"Bydgoszcz, Poland","name":"ESORICS: European Symposium on Research in Computer Security","start_date":"2024-09-16"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_created":"2025-04-20T22:01:28Z","acknowledgement":"This work was supported in part by the ERC CoG 863818 (ForM-SMArt), Austrian Science Fund (FWF) 10.55776/COE12, and MOE-T2EP20122-0014 (Data-Driven Distributed Algorithms) grants.","doi":"10.1007/978-3-031-82349-7_15","year":"2025","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031823480"],"issn":["0302-9743"]},"publication_status":"published","title":"Route discovery in private payment channel networks","type":"conference","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"language":[{"iso":"eng"}]},{"acknowledgement":"We thank S. Woudenberg, S. Valk and J. Rienstra for help and advice, A. Kuhn for comments on the paper and M. Prigge and M. Estelle for helpful discussions. This work was supported by a grant from Netherlands Organization for Scientific Research (NWO; OCENW.M20.031 to J.W.B.), a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2020 contract number to J.H.G.) and a research grant from the Human Frontiers Research Program (HFSP; grant RGP0015/2022 to D.W.).","doi":"10.1038/s41477-025-01975-1","year":"2025","publication_identifier":{"eissn":["2055-0278"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","type":"journal_article","title":"ARF degradation defines a deeply conserved step in auxin response","language":[{"iso":"eng"}],"publication_status":"published","article_type":"letter_note","author":[{"last_name":"De Roij","full_name":"De Roij, Martijn","first_name":"Martijn"},{"last_name":"Hernández García","full_name":"Hernández García, Jorge","first_name":"Jorge"},{"last_name":"Das","full_name":"Das, Shubhajit","id":"b08969a4-f2a5-11ed-b6c4-ff0f10b7d0be","first_name":"Shubhajit"},{"first_name":"Jan Willem","last_name":"Borst","full_name":"Borst, Jan Willem"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"day":"11","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In land plants, the signalling molecule auxin profoundly controls growth and development, chiefly through a transcriptional response system. The auxin response is mediated by modulating the activity of DNA-binding auxin response factor (ARF) proteins. The concentrations and stoichiometry of the competing A- and B-class ARFs define cells’ capacity for auxin response. In the minimal auxin response system of the liverwort Marchantia polymorpha, both A- and B-ARFs are unstable, but the underlying mechanisms, developmental relevance and evolutionary history of this instability are unknown. Here we identify a minimal motif that is necessary for MpARF2 (B-class) degradation and show that it is critical for development and the auxin response. Through comparative analysis and motif swaps among all ARF classes in extant algae and land plants, we infer that the emergence of ARF instability probably occurred in the ancestor of the A- and B-ARF clades and, therefore, preceded or coincided with the origin of the auxin response system."}],"publication":"Nature Plants","external_id":{"pmid":["40216983"]},"date_published":"2025-04-11T00:00:00Z","file":[{"file_id":"20882","file_name":"2025_NaturePlants_deRoij.pdf","relation":"main_file","access_level":"open_access","checksum":"8225c1899bb2f39f9a1707cc0697a052","content_type":"application/pdf","date_created":"2025-12-30T07:28:09Z","success":1,"file_size":7062474,"creator":"dernst","date_updated":"2025-12-30T07:28:09Z"}],"date_updated":"2025-12-30T07:28:49Z","oa":1,"scopus_import":"1","file_date_updated":"2025-12-30T07:28:09Z","department":[{"_id":"JiFr"}],"ddc":["580"],"status":"public","_id":"19601","page":"717-724","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","volume":11,"OA_type":"hybrid","quality_controlled":"1","citation":{"ama":"De Roij M, Hernández García J, Das S, Borst JW, Weijers D. ARF degradation defines a deeply conserved step in auxin response. <i>Nature Plants</i>. 2025;11:717-724. doi:<a href=\"https://doi.org/10.1038/s41477-025-01975-1\">10.1038/s41477-025-01975-1</a>","chicago":"De Roij, Martijn, Jorge Hernández García, Shubhajit Das, Jan Willem Borst, and Dolf Weijers. “ARF Degradation Defines a Deeply Conserved Step in Auxin Response.” <i>Nature Plants</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41477-025-01975-1\">https://doi.org/10.1038/s41477-025-01975-1</a>.","ieee":"M. De Roij, J. Hernández García, S. Das, J. W. Borst, and D. Weijers, “ARF degradation defines a deeply conserved step in auxin response,” <i>Nature Plants</i>, vol. 11. Springer Nature, pp. 717–724, 2025.","apa":"De Roij, M., Hernández García, J., Das, S., Borst, J. W., &#38; Weijers, D. (2025). ARF degradation defines a deeply conserved step in auxin response. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-025-01975-1\">https://doi.org/10.1038/s41477-025-01975-1</a>","mla":"De Roij, Martijn, et al. “ARF Degradation Defines a Deeply Conserved Step in Auxin Response.” <i>Nature Plants</i>, vol. 11, Springer Nature, 2025, pp. 717–24, doi:<a href=\"https://doi.org/10.1038/s41477-025-01975-1\">10.1038/s41477-025-01975-1</a>.","short":"M. De Roij, J. Hernández García, S. Das, J.W. Borst, D. Weijers, Nature Plants 11 (2025) 717–724.","ista":"De Roij M, Hernández García J, Das S, Borst JW, Weijers D. 2025. ARF degradation defines a deeply conserved step in auxin response. Nature Plants. 11, 717–724."},"has_accepted_license":"1","intvolume":"        11","publisher":"Springer Nature","month":"04","OA_place":"publisher"},{"article_type":"original","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"bdb51a6e-d553-11ed-ba76-c2025f3d5725","grant_number":"804981","name":"Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants"}],"type":"journal_article","title":"Extensive N4 cytosine methylation is essential for Marchantia sperm function","date_created":"2025-04-20T22:01:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"year":"2025","doi":"10.1016/j.cell.2025.03.014","acknowledgement":"We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the High Performance Computing resources provided by the ISTA Scientific Computing Facility and Norwich BioScience Institute Partnership Computing Infrastructure. This work was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111 to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship (S.X.), and ISTA core funding (Y.Y. and X.F.).","external_id":{"isi":["001504744800006"],"pmid":["40209706"]},"date_published":"2025-05-29T00:00:00Z","file":[{"date_updated":"2025-12-29T13:40:32Z","creator":"dernst","file_size":11622960,"success":1,"content_type":"application/pdf","date_created":"2025-12-29T13:40:32Z","checksum":"0dcc2feb368dfe7c4890093366b2dacb","access_level":"open_access","relation":"main_file","file_name":"2025_Cell_Walker.pdf","file_id":"20871"}],"publication":"Cell","abstract":[{"lang":"eng","text":"N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance and even its presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC) expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis. Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and fertility defects, and impairs post-fertilization development. Our results reveal extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases, and elucidate the biological functions of 4mC in reproductive development, thereby expanding the repertoire of functional eukaryotic DNA modifications."}],"issue":"11","oa_version":"Published Version","pmid":1,"day":"29","PlanS_conform":"1","author":[{"last_name":"Walker","full_name":"Walker, James","first_name":"James"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"first_name":"Yalin","full_name":"Liu, Yalin","last_name":"Liu"},{"last_name":"Xu","full_name":"Xu, Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","first_name":"Shujuan"},{"orcid":"0000-0002-9919-7282","first_name":"Yiming","id":"318e643b-8b61-11ed-b69e-aafa103ec8dd","full_name":"Yu, Yiming","last_name":"Yu"},{"first_name":"Martin","last_name":"Vickers","full_name":"Vickers, Martin"},{"first_name":"Weizhi","id":"fec73395-8b60-11ed-b69e-927fda99c743","full_name":"Ouyang, Weizhi","last_name":"Ouyang"},{"full_name":"Tálas, Judit","last_name":"Tálas","first_name":"Judit"},{"last_name":"Dolan","full_name":"Dolan, Liam","first_name":"Liam"},{"first_name":"Keiji","full_name":"Nakajima, Keiji","last_name":"Nakajima"},{"orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng"}],"corr_author":"1","_id":"19602","status":"public","ddc":["570"],"department":[{"_id":"XiFe"}],"file_date_updated":"2025-12-29T13:40:32Z","scopus_import":"1","oa":1,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/"}]},"date_updated":"2026-04-28T13:36:51Z","OA_place":"publisher","month":"05","publisher":"Elsevier","intvolume":"       188","has_accepted_license":"1","citation":{"mla":"Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>, vol. 188, no. 11, Elsevier, 2025, p. 2890–2906.e14, doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>.","apa":"Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025). Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>","ista":"Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for Marchantia sperm function. Cell. 188(11), 2890–2906.e14.","short":"J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas, L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14.","chicago":"Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers, Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia Sperm Function.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">https://doi.org/10.1016/j.cell.2025.03.014</a>.","ama":"Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential for Marchantia sperm function. <i>Cell</i>. 2025;188(11):2890-2906.e14. doi:<a href=\"https://doi.org/10.1016/j.cell.2025.03.014\">10.1016/j.cell.2025.03.014</a>","ieee":"J. Walker <i>et al.</i>, “Extensive N4 cytosine methylation is essential for Marchantia sperm function,” <i>Cell</i>, vol. 188, no. 11. Elsevier, p. 2890–2906.e14, 2025."},"volume":188,"OA_type":"hybrid","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"2890-2906.e14"},{"oa_version":"Published Version","author":[{"first_name":"Jonas","full_name":"Lill, Jonas","last_name":"Lill"},{"id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","first_name":"Kalina H","last_name":"Petrova","full_name":"Petrova, Kalina H"},{"first_name":"Simon","last_name":"Weber","full_name":"Weber, Simon"}],"day":"01","publication":"Algorithmica","external_id":{"isi":["001463103800001"]},"date_published":"2025-07-01T00:00:00Z","file":[{"file_id":"20957","file_name":"2025_Algorithmica_Lill.pdf","access_level":"open_access","relation":"main_file","checksum":"eab3f1834b0ba347b05ae9897729c0ad","content_type":"application/pdf","date_created":"2026-01-05T13:45:57Z","success":1,"file_size":448554,"creator":"dernst","date_updated":"2026-01-05T13:45:57Z"}],"abstract":[{"text":"MaxCut is a classical NP-complete problem and a crucial building block in many\r\ncombinatorial algorithms. The famousEdwards-Erdös bound states that any connected\r\ngraph on n vertices with m edges contains a cut of size at least m/2 + n−1/4 . Crowston,\r\nJones and Mnich [Algorithmica, 2015] showed that the MaxCut problem on simple\r\nconnected graphs admits an FPT algorithm, where the parameter k is the difference\r\nbetween the desired cut size c and the lower bound given by the Edwards-Erdös\r\nbound. This was later improved by Etscheid and Mnich [Algorithmica, 2017] to run\r\nin parameterized linear time, i.e., f (k) · O(m). We improve upon this result in two\r\nways: Firstly, we extend the algorithm to work also for multigraphs (alternatively,\r\ngraphs with positive integer weights). Secondly, we change the parameter; instead of\r\nthe difference to the Edwards-Erdös bound, we use the difference to the Poljak-Turzík\r\nbound. The Poljak-Turzík bound states that any weighted graph G has a cut of weight\r\nat least w(G)/2 + wMSF (G)/4 , where w(G) denotes the total weight of G, and wMSF (G)\r\ndenotes the weight of its minimum spanning forest. In connected simple graphs the\r\ntwo bounds are equivalent, but for multigraphs the Poljak-Turzík bound can be larger\r\nand thus yield a smaller parameter k. Our algorithm also runs in parameterized linear\r\ntime, i.e., f (k) · O(m + n).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-20T22:01:28Z","acknowledgement":"Kalina Petrova is supported by the Swiss National Science Foundation, grant no. CRSII5 173721, and also receives funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Simon Weber is supported by the Swiss National Science Foundation under project no. 204320.\r\nOpen access funding provided by Swiss Federal Institute of Technology Zurich.","doi":"10.1007/s00453-025-01306-y","year":"2025","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"publication_status":"published","article_type":"original","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"title":"Linear-time MaxCut in multigraphs parameterized above the Poljak-Turzík bound","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","OA_type":"hybrid","volume":87,"has_accepted_license":"1","citation":{"short":"J. Lill, K.H. Petrova, S. Weber, Algorithmica 87 (2025) 983–1007.","ista":"Lill J, Petrova KH, Weber S. 2025. Linear-time MaxCut in multigraphs parameterized above the Poljak-Turzík bound. Algorithmica. 87, 983–1007.","apa":"Lill, J., Petrova, K. H., &#38; Weber, S. (2025). Linear-time MaxCut in multigraphs parameterized above the Poljak-Turzík bound. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-025-01306-y\">https://doi.org/10.1007/s00453-025-01306-y</a>","mla":"Lill, Jonas, et al. “Linear-Time MaxCut in Multigraphs Parameterized above the Poljak-Turzík Bound.” <i>Algorithmica</i>, vol. 87, Springer Nature, 2025, pp. 983–1007, doi:<a href=\"https://doi.org/10.1007/s00453-025-01306-y\">10.1007/s00453-025-01306-y</a>.","ieee":"J. Lill, K. H. Petrova, and S. Weber, “Linear-time MaxCut in multigraphs parameterized above the Poljak-Turzík bound,” <i>Algorithmica</i>, vol. 87. Springer Nature, pp. 983–1007, 2025.","ama":"Lill J, Petrova KH, Weber S. Linear-time MaxCut in multigraphs parameterized above the Poljak-Turzík bound. <i>Algorithmica</i>. 2025;87:983-1007. doi:<a href=\"https://doi.org/10.1007/s00453-025-01306-y\">10.1007/s00453-025-01306-y</a>","chicago":"Lill, Jonas, Kalina H Petrova, and Simon Weber. “Linear-Time MaxCut in Multigraphs Parameterized above the Poljak-Turzík Bound.” <i>Algorithmica</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00453-025-01306-y\">https://doi.org/10.1007/s00453-025-01306-y</a>."},"page":"983-1007","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"OA_place":"publisher","month":"07","intvolume":"        87","publisher":"Springer Nature","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"18758"}]},"oa":1,"date_updated":"2026-01-05T13:46:08Z","status":"public","_id":"19603","scopus_import":"1","ddc":["510"],"department":[{"_id":"MaKw"}],"file_date_updated":"2026-01-05T13:45:57Z"},{"oa":1,"date_updated":"2025-09-30T12:17:33Z","status":"public","_id":"19617","corr_author":"1","scopus_import":"1","file_date_updated":"2025-04-24T06:40:22Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ddc":["539"],"OA_type":"hybrid","quality_controlled":"1","volume":23,"citation":{"short":"S. Hawaldar, S.S. Khaire, P. Delsing, B. Suri, Physical Review Applied 23 (2025).","ista":"Hawaldar S, Khaire SS, Delsing P, Suri B. 2025. On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability. Physical Review Applied. 23(4), 044042.","apa":"Hawaldar, S., Khaire, S. S., Delsing, P., &#38; Suri, B. (2025). On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevapplied.23.044042\">https://doi.org/10.1103/physrevapplied.23.044042</a>","mla":"Hawaldar, Samarth, et al. “On-Demand Single-Microwave-Photon Source in a Superconducting Circuit with Wideband Frequency Tunability.” <i>Physical Review Applied</i>, vol. 23, no. 4, 044042, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/physrevapplied.23.044042\">10.1103/physrevapplied.23.044042</a>.","ieee":"S. Hawaldar, S. S. Khaire, P. Delsing, and B. Suri, “On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability,” <i>Physical Review Applied</i>, vol. 23, no. 4. American Physical Society, 2025.","chicago":"Hawaldar, Samarth, Siddhi Satish Khaire, Per Delsing, and Baladitya Suri. “On-Demand Single-Microwave-Photon Source in a Superconducting Circuit with Wideband Frequency Tunability.” <i>Physical Review Applied</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/physrevapplied.23.044042\">https://doi.org/10.1103/physrevapplied.23.044042</a>.","ama":"Hawaldar S, Khaire SS, Delsing P, Suri B. On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability. <i>Physical Review Applied</i>. 2025;23(4). doi:<a href=\"https://doi.org/10.1103/physrevapplied.23.044042\">10.1103/physrevapplied.23.044042</a>"},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","month":"04","OA_place":"publisher","intvolume":"        23","publisher":"American Physical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-04-24T06:34:07Z","acknowledgement":"The authors acknowledge the support of DST-INSPIRE Fellowship No. IF180339 and DST-SERB Core Research Grant No. CRG/2018/002129. S.H. acknowledges the support of the Kishore Vaigyanik Protsahan Yojana (KVPY). S.H. also acknowledges helpful discussions with Harsh Arora and Johannes Fink.","doi":"10.1103/physrevapplied.23.044042","article_number":"044042","year":"2025","publication_identifier":{"issn":["2331-7019"]},"publication_status":"published","article_type":"original","type":"journal_article","title":"On-demand single-microwave-photon source in a superconducting circuit with wideband frequency tunability","isi":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","issue":"4","author":[{"orcid":"0000-0002-1965-4309","last_name":"Hawaldar","full_name":"Hawaldar, Samarth","id":"221708e1-1ff6-11ee-9fa6-85146607433e","first_name":"Samarth"},{"last_name":"Khaire","full_name":"Khaire, Siddhi Satish","first_name":"Siddhi Satish"},{"first_name":"Per","full_name":"Delsing, Per","last_name":"Delsing"},{"first_name":"Baladitya","full_name":"Suri, Baladitya","last_name":"Suri"}],"day":"18","publication":"Physical Review Applied","file":[{"access_level":"open_access","relation":"main_file","file_id":"19620","file_name":"PhysRevApplied.23.044042.pdf","checksum":"582b2ed6afb654300cabf0e3add14ca8","file_size":837219,"content_type":"application/pdf","date_created":"2025-04-24T06:40:22Z","success":1,"date_updated":"2025-04-24T06:40:22Z","creator":"shawalda"}],"date_published":"2025-04-18T00:00:00Z","external_id":{"isi":["001490745300002"]},"abstract":[{"text":"In this article, we propose a method for generating single microwave photons in superconducting circuits. We theoretically show that pure single microwave photons can be generated on demand and tuned over a large frequency band by making use of Landau-Zener transitions under a rapid sweep of a control parameter. We devise a protocol that enables fast control of the frequency of the emitted photon over two octaves, without requiring extensive calibration. Additionally, we make theoretical estimates of the generation efficiency, tunability, purity, and linewidth of the photons emitted using this method for both charge- and flux-qubit-based architectures. We also provide estimates of the optimal device parameters required for these architectures to realize the device.","lang":"eng"}]},{"date_published":"2025-04-10T00:00:00Z","file":[{"date_updated":"2025-05-05T06:57:49Z","creator":"dernst","file_size":424364,"content_type":"application/pdf","date_created":"2025-05-05T06:57:49Z","success":1,"checksum":"f6541ea1736a7413c6d24f14d64a4dda","access_level":"open_access","relation":"main_file","file_id":"19644","file_name":"2025_RepresentationTheory_Nessonov.pdf"}],"external_id":{"arxiv":["2206.01964"]},"publication":"Representation Theory","abstract":[{"lang":"eng","text":"In this paper we obtain a complete description of all indecomposable characters (central positive-definite functions) of inductive limits of the symmetric groups under block diagonal embedding. As a corollary we obtain the full classification of the isomorphism classes of these inductive limits."}],"issue":"8","oa_version":"Published Version","day":"10","author":[{"first_name":"Nikolay","full_name":"Nessonov, Nikolay","last_name":"Nessonov"},{"id":"28e53c8c-896a-11ed-bdf8-f809043ce2f0","first_name":"Nhok T","last_name":"Ngo","full_name":"Ngo, Nhok T"}],"article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Geometry of the tip of the global nilpotent cone","grant_number":"P35847","_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3"}],"title":"Indecomposable characters of inductive limits of symmetric groups","type":"journal_article","license":"https://creativecommons.org/licenses/by/3.0/","date_created":"2025-04-24T08:48:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1088-4165"]},"year":"2025","acknowledgement":"The authors were partially supported by the “Long-term program of support of the Ukrainian research teams at the Polish Academy of Sciences carried out in collaboration with the U.S. National Academy of Sciences with the financial support of external partners”. The second author was also supported by the Austrian Science Fund (FWF) grant “Geometry of the tip of the global nilpotent cone” no. 10.55776/P35847","doi":"10.1090/ert/689","OA_place":"publisher","month":"04","publisher":"American Mathematical Society","intvolume":"        29","has_accepted_license":"1","citation":{"mla":"Nessonov, Nikolay, and Nhok T. Ngo. “Indecomposable Characters of Inductive Limits of Symmetric Groups.” <i>Representation Theory</i>, vol. 29, no. 8, American Mathematical Society, 2025, pp. 256–88, doi:<a href=\"https://doi.org/10.1090/ert/689\">10.1090/ert/689</a>.","apa":"Nessonov, N., &#38; Ngo, N. T. (2025). Indecomposable characters of inductive limits of symmetric groups. <i>Representation Theory</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/ert/689\">https://doi.org/10.1090/ert/689</a>","short":"N. Nessonov, N.T. Ngo, Representation Theory 29 (2025) 256–288.","ista":"Nessonov N, Ngo NT. 2025. Indecomposable characters of inductive limits of symmetric groups. Representation Theory. 29(8), 256–288.","chicago":"Nessonov, Nikolay, and Nhok T Ngo. “Indecomposable Characters of Inductive Limits of Symmetric Groups.” <i>Representation Theory</i>. American Mathematical Society, 2025. <a href=\"https://doi.org/10.1090/ert/689\">https://doi.org/10.1090/ert/689</a>.","ama":"Nessonov N, Ngo NT. Indecomposable characters of inductive limits of symmetric groups. <i>Representation Theory</i>. 2025;29(8):256-288. doi:<a href=\"https://doi.org/10.1090/ert/689\">10.1090/ert/689</a>","ieee":"N. Nessonov and N. T. Ngo, “Indecomposable characters of inductive limits of symmetric groups,” <i>Representation Theory</i>, vol. 29, no. 8. American Mathematical Society, pp. 256–288, 2025."},"volume":29,"quality_controlled":"1","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"page":"256-288","_id":"19621","corr_author":"1","status":"public","ddc":["510"],"file_date_updated":"2025-05-05T06:57:49Z","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"arxiv":1,"scopus_import":"1","oa":1,"date_updated":"2025-05-05T06:59:07Z"},{"author":[{"first_name":"Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","full_name":"Desaules, Jean-Yves Marc","last_name":"Desaules","orcid":"0000-0002-3749-6375"}],"day":"24","oa_version":"Published Version","abstract":[{"text":"Persistent revivals recently observed in Rydberg atom simulators have challenged our understanding of thermalization and attracted much interest to the concept of quantum many-body scars (QMBSs). QMBSs are non-thermal highly excited eigenstates that coexist with typical eigenstates in the spectrum of many-body Hamiltonians, and have since been reported in multiple theoretical models, including the so-called PXP model, approximately realized by Rydberg simulators. At the same time, questions of how common QMBSs are and in what models they are physically realized remain open. In this Letter, we demonstrate that QMBSs exist in a broader family of models that includes and generalizes PXP to longer-range constraints and states with different periodicity. We show that in each model, multiple QMBS families can be found. Each of them relies on a different approximate 𝔰𝔲⁡(2) algebra, leading to oscillatory dynamics in all cases. However, in contrast to the PXP model, their observation requires launching dynamics from weakly entangled initial states rather than from a product state. QMBSs reported here may be experimentally probed using Rydberg atom simulator in the regime of longer-range Rydberg blockades.","lang":"eng"}],"date_published":"2025-04-24T00:00:00Z","file":[{"checksum":"d073314c4dc95d93feaadbff188ce4a1","relation":"main_file","access_level":"open_access","file_id":"19646","file_name":"Data+Code.zip","date_updated":"2025-05-05T07:14:17Z","creator":"jdesaule","file_size":583478621,"date_created":"2025-05-05T07:14:17Z","content_type":"application/zip","success":1},{"creator":"jdesaule","date_updated":"2025-05-05T07:13:46Z","date_created":"2025-05-05T07:13:46Z","content_type":"text/plain","success":1,"file_size":15856,"checksum":"d386a2364fb1147ef6dad30ad029c080","file_id":"19647","file_name":"readme.txt","relation":"main_file","access_level":"open_access"}],"keyword":["quantum many-body scars","non-equilibrium physics","Rydberg atoms"],"doi":"10.15479/AT:ISTA:19623","acknowledgement":"The authors are grateful to Zlatko Papić, Dolev Bluvstein, Nishad Maskara, Marcello Dalmonte, Thomas Iadecola, and Johannes Feldmeier for insightful discussions. A. K., M. L., and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). J.-Y. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2025","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_created":"2025-04-24T19:58:46Z","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"type":"research_data","title":"Research Data for \"Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators\"","ec_funded":1,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"has_accepted_license":"1","citation":{"apa":"Desaules, J.-Y. M. (2025). Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:19623\">https://doi.org/10.15479/AT:ISTA:19623</a>","mla":"Desaules, Jean-Yves Marc. <i>Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19623\">10.15479/AT:ISTA:19623</a>.","ista":"Desaules J-YM. 2025. Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:19623\">10.15479/AT:ISTA:19623</a>.","short":"J.-Y.M. Desaules, (2025).","ama":"Desaules J-YM. Research Data for “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:19623\">10.15479/AT:ISTA:19623</a>","chicago":"Desaules, Jean-Yves Marc. “Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:19623\">https://doi.org/10.15479/AT:ISTA:19623</a>.","ieee":"J.-Y. M. Desaules, “Research Data for ‘Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.’” Institute of Science and Technology Austria, 2025."},"publisher":"Institute of Science and Technology Austria","month":"04","date_updated":"2026-06-10T08:40:52Z","oa":1,"related_material":{"record":[{"id":"19664","status":"public","relation":"used_in_publication"}]},"ddc":["530"],"department":[{"_id":"MaSe"}],"file_date_updated":"2025-05-05T07:14:17Z","status":"public","contributor":[{"last_name":"Kerschbaumer","first_name":"Aron","id":"ade85a9c-3200-11ee-973b-91c1eb240410","contributor_type":"researcher"},{"last_name":"Ljubotina","first_name":"Marko","contributor_type":"researcher"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Maksym"},{"last_name":"Desaules","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","contributor_type":"researcher","first_name":"Jean-Yves Marc","orcid":"0000-0002-3749-6375"}],"corr_author":"1","_id":"19623"},{"date_updated":"2025-09-30T12:19:22Z","oa":1,"file_date_updated":"2025-05-05T09:20:54Z","department":[{"_id":"JaMa"}],"ddc":["510"],"arxiv":1,"scopus_import":"1","corr_author":"1","_id":"19625","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","citation":{"short":"R.R. Kumar, M. Wirth, Communications in Mathematical Physics 406 (2025).","ista":"Kumar RR, Wirth M. 2025. Operator-valued twisted Araki–Woods algebras. Communications in Mathematical Physics. 406(5), 110.","mla":"Kumar, R. Rahul, and Melchior Wirth. “Operator-Valued Twisted Araki–Woods Algebras.” <i>Communications in Mathematical Physics</i>, vol. 406, no. 5, 110, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00220-025-05285-7\">10.1007/s00220-025-05285-7</a>.","apa":"Kumar, R. R., &#38; Wirth, M. (2025). Operator-valued twisted Araki–Woods algebras. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-025-05285-7\">https://doi.org/10.1007/s00220-025-05285-7</a>","ieee":"R. R. Kumar and M. Wirth, “Operator-valued twisted Araki–Woods algebras,” <i>Communications in Mathematical Physics</i>, vol. 406, no. 5. Springer Nature, 2025.","chicago":"Kumar, R. Rahul, and Melchior Wirth. “Operator-Valued Twisted Araki–Woods Algebras.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00220-025-05285-7\">https://doi.org/10.1007/s00220-025-05285-7</a>.","ama":"Kumar RR, Wirth M. Operator-valued twisted Araki–Woods algebras. <i>Communications in Mathematical Physics</i>. 2025;406(5). doi:<a href=\"https://doi.org/10.1007/s00220-025-05285-7\">10.1007/s00220-025-05285-7</a>"},"has_accepted_license":"1","volume":406,"OA_type":"hybrid","quality_controlled":"1","publisher":"Springer Nature","intvolume":"       406","month":"05","OA_place":"publisher","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"year":"2025","article_number":"110","acknowledgement":"The authors want to thank the organizers of YMC*A 2023 in Leuven, where this collaboration was conceived. They are grateful to Dan Voiculescu for a valuable historical remark and to Zhiyuan Yang for raising the question if operator-valued weights give rise to Tomita correspondences. R.K. was funded by IIT Kanpur through the Institute Postdoctoral Fellowship. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission.\r\nOpen Access funding enabled and organized by Projekt DEAL.","doi":"10.1007/s00220-025-05285-7","date_created":"2025-04-27T22:02:13Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","title":"Operator-valued twisted Araki–Woods algebras","project":[{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"article_type":"original","publication_status":"published","day":"01","author":[{"last_name":"Kumar","full_name":"Kumar, R. Rahul","first_name":"R. Rahul"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241"}],"issue":"5","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We introduce operator-valued twisted Araki–Woods algebras. These are operator-valued versions of a class of second quantization algebras that includes q-Gaussian and q-Araki–Woods algebras and also generalize Shlyakhtenko’s von Neumann algebras generated by operator-valued semicircular variables. We develop a disintegration theory that reduces the isomorphism type of operator-valued twisted Araki–Woods algebras over type I factors to the scalar-valued case. Moreover, these algebras come with a natural weight, and we characterize its modular theory. We also give sufficient criteria that guarantee the factoriality of these algebras."}],"file":[{"file_size":650764,"content_type":"application/pdf","date_created":"2025-05-05T09:20:54Z","success":1,"date_updated":"2025-05-05T09:20:54Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"19650","file_name":"2025_CommMathPhysics_Kumar.pdf","checksum":"2948e8f567f20f5f837061d2c775534f"}],"date_published":"2025-05-01T00:00:00Z","external_id":{"arxiv":["2406.06179"],"isi":["001464170400003"],"pmid":["40225194"]},"publication":"Communications in Mathematical Physics"},{"publication":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["40193613"],"isi":["001471235200001"]},"file":[{"file_size":2949523,"date_created":"2025-06-24T07:27:43Z","content_type":"application/pdf","success":1,"date_updated":"2025-06-24T07:27:43Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"19888","file_name":"2025_PNAS_Jain.pdf","checksum":"115a687f40009660eb4b38b4f6559d41"}],"date_published":"2025-04-15T00:00:00Z","abstract":[{"text":"Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of nonfunctional “promoter leakiness,” merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the noncanonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g., control of costly-to-induce multidrug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multidrug resistance is crucial for effective public health measures.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"15","author":[{"id":"330F0278-F248-11E8-B48F-1D18A9856A87","first_name":"Kirti","last_name":"Jain","full_name":"Jain, Kirti","orcid":"0000-0002-3809-0449"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0003-1006-6639","last_name":"Bochkareva","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"orcid":"0000-0001-9480-5261","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","first_name":"Roderich","last_name":"Römhild","full_name":"Römhild, Roderich"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"APC_amount":"5949 EUR","day":"15","publication_status":"published","article_type":"original","project":[{"name":"Tools for automation and feedback microscopy","grant_number":"CZI01","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473"},{"_id":"bd6f94d1-d553-11ed-ba76-ae9f07250f74","name":"Non-canonical antibiotic interactions","grant_number":"E219"},{"_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation","grant_number":"I05127"}],"title":"Pulsatile basal gene expression as a fitness determinant in bacteria","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-04-27T22:02:13Z","acknowledgement":"K.J. thanks B. Wu, I. Tomanek, K. Tomasek for detailed discussions on the manuscript, all other members from the Guet laboratory for valuable feedback, R. Chait, & Imaging and Optics Facility, Institute of Science and Technology Austria for helping with microscopy, Dr. Sudha Rao and Dr. Raja Mugasimangalam, Genotypic Technology India for allowing time off to address the revisions. K.J. acknowledges Institute of Science and Technology fellowship IC1006FELL02, R.H. was supported in part by Chan Zuckerberg Initiative and Donor Advised-Fund grant 2020-225401 (https://doi.org/10.37921/120055ratwvi), O.O.B. acknowledges Fonds Zur Förderung der Wissenschaftlichen Forschung (FWF) Grant ESP253-B, R.R. acknowledges FWF Grant 10.55776/ESP219, C.C.G. acknowledges FWF I5127-B.","doi":"10.1073/pnas.2413709122","article_number":"e2413709122","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2025","OA_place":"publisher","month":"04","intvolume":"       122","publisher":"National Academy of Sciences","OA_type":"hybrid","volume":122,"quality_controlled":"1","has_accepted_license":"1","citation":{"ieee":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Pulsatile basal gene expression as a fitness determinant in bacteria,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of Sciences, 2025.","chicago":"Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper Tkačik, and Calin C Guet. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>.","ama":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(15). doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>","ista":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Pulsatile basal gene expression as a fitness determinant in bacteria. Proceedings of the National Academy of Sciences. 122(15), e2413709122.","short":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, Proceedings of the National Academy of Sciences 122 (2025).","mla":"Jain, Kirti, et al. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15, e2413709122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>.","apa":"Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet, C. C. (2025). Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>"},"article_processing_charge":"Yes (in subscription journal)","acknowledged_ssus":[{"_id":"Bio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","_id":"19626","corr_author":"1","scopus_import":"1","ddc":["570"],"file_date_updated":"2025-06-24T07:27:43Z","department":[{"_id":"CaGu"},{"_id":"Bio"},{"_id":"FyKo"},{"_id":"GaTk"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"19294"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/clockwork-just-for-antibiotic-resistance/","description":"News on ISTA website"}]},"oa":1,"date_updated":"2026-05-20T08:33:08Z"}]