[{"dataavailabilitystatement":"The training scripts, trained CACE potentials, and MD input files are available at https://github.com/BingqingCheng/cace-lr-fit.","has_accepted_license":"1","intvolume":"        11","supplementarymaterial":"no","publication_status":"published","publisher":"Springer Nature","type":"journal_article","corr_author":"1","citation":{"apa":"Cheng, B. (2025). Latent Ewald summation for machine learning of long-range interactions. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>","mla":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>, vol. 11, 80, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>.","ista":"Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions. npj Computational Materials. 11, 80.","ieee":"B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,” <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025.","chicago":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>.","short":"B. Cheng, Npj Computational Materials 11 (2025).","ama":"Cheng B. Latent Ewald summation for machine learning of long-range interactions. <i>npj Computational Materials</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>"},"abstract":[{"text":"Machine learning interatomic potentials (MLIPs) often neglect long-range interactions, such as electrostatic and dispersion forces. In this work, we introduce a straightforward and efficient method to account for long-range interactions by learning a hidden variable from local atomic descriptors and applying an Ewald summation to this variable. We demonstrate that in systems including charged and polar molecular dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can lead to unphysical predictions even when employing message passing. The long-range models effectively eliminate these artifacts, with only about twice the computational cost of short-range MLIPs.","lang":"eng"}],"scopus_import":"1","doi":"10.1038/s41524-025-01577-7","month":"03","file_date_updated":"2025-04-08T09:34:58Z","article_processing_charge":"Yes","isi":1,"language":[{"iso":"eng"}],"volume":11,"quality_controlled":"1","ddc":["000"],"year":"2025","publication":"npj Computational Materials","file":[{"file_size":1608315,"checksum":"cc99b7407a12139d9b2d8457961935ae","date_created":"2025-04-08T09:34:58Z","relation":"main_file","file_name":"2025_npjCompMaterials_Cheng.pdf","creator":"dernst","file_id":"19528","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2025-04-08T09:34:58Z"}],"date_created":"2025-04-06T22:01:32Z","oa_version":"Published Version","article_number":"80","_id":"19495","oa":1,"researchdata_availability":"unclear","external_id":{"isi":["001453622900002"],"arxiv":["2408.15165"]},"DOAJ_listed":"1","date_published":"2025-03-26T00:00:00Z","arxiv":1,"OA_type":"gold","publication_identifier":{"eissn":["2057-3960"]},"acknowledgement":"B. C. thanks David Limmer for providing the water slab dataset, and Carolin Faller for the NaCl dataset.","OA_place":"publisher","article_type":"original","das_tickbox":"1","day":"26","department":[{"_id":"BiCh"}],"title":"Latent Ewald summation for machine learning of long-range interactions","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"status":"public","date_updated":"2026-08-07T10:04:17Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"OA_type":"hybrid","publication_identifier":{"eissn":["1091-6490"]},"date_published":"2025-12-02T00:00:00Z","external_id":{"pmid":["41269783"]},"researchdata_availability":"no","oa":1,"pmid":1,"_id":"20702","oa_version":"Published Version","article_number":"e2510235122","date_created":"2025-11-30T23:02:06Z","file":[{"relation":"main_file","date_created":"2025-12-01T08:41:32Z","checksum":"58051539a884c7a97306fd3afdb539ac","file_size":27607870,"creator":"dernst","file_name":"2025_PNAS_King.pdf","file_id":"20719","date_updated":"2025-12-01T08:41:32Z","content_type":"application/pdf","success":1,"access_level":"open_access"}],"publication":"Proceedings of the National Academy of Sciences","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2026-08-07T10:27:53Z","status":"public","author":[{"last_name":"King","first_name":"Daniel S.","full_name":"King, Daniel S."},{"full_name":"Grzenda, Daniel","first_name":"Daniel","last_name":"Grzenda"},{"first_name":"Ray","last_name":"Zhu","full_name":"Zhu, Ray"},{"full_name":"Hudson, Nathaniel","last_name":"Hudson","first_name":"Nathaniel"},{"full_name":"Foster, Ian","first_name":"Ian","last_name":"Foster"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Gagliardi, Laura","last_name":"Gagliardi","first_name":"Laura"}],"title":"Cartesian equivariant representations for learning and understanding molecular orbitals","day":"02","department":[{"_id":"BiCh"}],"das_tickbox":"1","OA_place":"publisher","article_type":"original","acknowledgement":"This work is supported as part of the Catalyst Design for Decarbonization Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under award no. DE-SC0023383. We thank the Research Computing Center at the University of Chicago and for access to computational resources. Additionally, this research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California (UC), Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). Furthermore, we thank Matthew Hennefarth and Matt Hermes for useful discussions.","related_material":{"link":[{"relation":"software","url":"https://github.com/GagliardiGroup/CEONet "}]},"doi":"10.1073/pnas.2510235122","scopus_import":"1","abstract":[{"text":"Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces.","lang":"eng"}],"citation":{"mla":"King, Daniel S., et al. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48, e2510235122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2510235122\">10.1073/pnas.2510235122</a>.","apa":"King, D. S., Grzenda, D., Zhu, R., Hudson, N., Foster, I., Cheng, B., &#38; Gagliardi, L. (2025). Cartesian equivariant representations for learning and understanding molecular orbitals. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2510235122\">https://doi.org/10.1073/pnas.2510235122</a>","ama":"King DS, Grzenda D, Zhu R, et al. Cartesian equivariant representations for learning and understanding molecular orbitals. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(48). doi:<a href=\"https://doi.org/10.1073/pnas.2510235122\">10.1073/pnas.2510235122</a>","short":"D.S. King, D. Grzenda, R. Zhu, N. Hudson, I. Foster, B. Cheng, L. Gagliardi, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"King, Daniel S., Daniel Grzenda, Ray Zhu, Nathaniel Hudson, Ian Foster, Bingqing Cheng, and Laura Gagliardi. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2510235122\">https://doi.org/10.1073/pnas.2510235122</a>.","ieee":"D. S. King <i>et al.</i>, “Cartesian equivariant representations for learning and understanding molecular orbitals,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48. National Academy of Sciences, 2025.","ista":"King DS, Grzenda D, Zhu R, Hudson N, Foster I, Cheng B, Gagliardi L. 2025. Cartesian equivariant representations for learning and understanding molecular orbitals. Proceedings of the National Academy of Sciences. 122(48), e2510235122."},"corr_author":"1","type":"journal_article","publisher":"National Academy of Sciences","publication_status":"published","supplementarymaterial":"no","intvolume":"       122","has_accepted_license":"1","dataavailabilitystatement":"Code has been deposited to https://github.com/GagliardiGroup/CEONet (83). Data has been deposited to https://doi.org/10.5281/zenodo.16934624 (84).","year":"2025","ddc":["540"],"quality_controlled":"1","volume":122,"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_processing_charge":"Yes (in subscription journal)","issue":"48","file_date_updated":"2025-12-01T08:41:32Z","month":"12"},{"type":"journal_article","corr_author":"1","publisher":"American Chemical Society","publication_status":"published","supplementarymaterial":"no","intvolume":"        21","related_material":{"link":[{"relation":"software","url":"https://github.com/tuoping/alchemicalFES"}]},"doi":"10.1021/acs.jctc.5c01248","scopus_import":"1","abstract":[{"lang":"eng","text":"Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES."}],"citation":{"ama":"Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. 2025;21(22):11427-11435. doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>","short":"P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435.","chicago":"Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>.","ieee":"P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.","ista":"Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435.","mla":"Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>.","apa":"Tuo, P., Zeng, Z., Chen, J., &#38; Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>"},"isi":1,"article_processing_charge":"No","issue":"22","page":"11427-11435","month":"10","year":"2025","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"volume":21,"language":[{"iso":"eng"}],"pmid":1,"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"_id":"20704","oa_version":"None","date_created":"2025-11-30T23:02:06Z","publication":"Journal of Chemical Theory and Computation","OA_type":"closed access","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"date_published":"2025-10-31T00:00:00Z","researchdata_availability":"no","external_id":{"isi":["001605927900001"],"pmid":["41172130"]},"author":[{"id":"6e5644c0-c180-11ed-a2da-facc4c9f4f09","first_name":"Ping","last_name":"Tuo","full_name":"Tuo, Ping"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu","orcid":"0000-0001-5126-4928"},{"id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875","first_name":"Jiale","last_name":"Chen"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"title":"Scalable multitemperature free energy sampling of classical Ising spin states","day":"31","department":[{"_id":"BiCh"},{"_id":"DaAl"}],"ec_funded":1,"das_tickbox":"0","article_type":"original","acknowledgement":"P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-08-07T10:29:06Z","status":"public"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-066-4"]},"date_published":"2025-09-15T00:00:00Z","file":[{"creator":"cchlebak","file_name":"2025_Ruzickova_Natalia_Thesis.zip","relation":"source_file","date_created":"2026-08-07T10:57:05Z","checksum":"0582508d439b233497384f83a8307398","file_size":56464803,"date_updated":"2026-08-07T10:57:05Z","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"22661"},{"embargo":"2026-09-15","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","embargo_to":"open_access","creator":"cchlebak","date_created":"2026-08-07T10:57:34Z","checksum":"b722289fd550abede63adc27b9c61784","file_size":30634378,"relation":"main_file","access_level":"closed","date_updated":"2026-08-07T10:57:34Z","content_type":"application/pdf","file_id":"22662"}],"_id":"20357","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"date_created":"2025-09-15T17:04:48Z","oa_version":"Published Version","keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"date_updated":"2026-08-10T07:47:56Z","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"15","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"degree_awarded":"PhD","acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","OA_place":"publisher","title":"Effect propagation in biological networks","author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova","first_name":"Natalia","full_name":"Ruzickova, Natalia"}],"alternative_title":["ISTA Thesis"],"citation":{"ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025.","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>"},"doi":"10.15479/AT-ISTA-20357","related_material":{"record":[{"relation":"part_of_dissertation","id":"18525","status":"public"}]},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","type":"dissertation","corr_author":"1","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"}],"doi_confirm":"1","publication_status":"published","language":[{"iso":"eng"}],"ddc":["570","530"],"year":"2025","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"file_date_updated":"2026-08-07T10:57:34Z","page":"156","month":"09","article_processing_charge":"No"},{"publication":"Journal of Neuroinflammation","file":[{"file_id":"19607","content_type":"application/pdf","success":1,"date_updated":"2025-04-22T09:46:27Z","access_level":"open_access","relation":"main_file","file_size":4482167,"checksum":"dcc355c21ab713e45fda5c61b5fa5299","date_created":"2025-04-22T09:46:27Z","creator":"dernst","file_name":"2025_JourNeuroinflammation_Schmied.pdf"}],"date_created":"2025-04-20T22:01:28Z","article_number":"98","oa_version":"Published Version","_id":"19593","pmid":1,"project":[{"_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"external_id":{"isi":["001459311800002"],"pmid":["40181459"]},"DOAJ_listed":"1","date_published":"2025-04-03T00:00:00Z","publication_identifier":{"eissn":["1742-2094"]},"OA_type":"gold","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.).","APC_amount":"3948 EUR","OA_place":"publisher","article_type":"original","day":"03","department":[{"_id":"SaSi"}],"author":[{"id":"32B7C918-F248-11E8-B48F-1D18A9856A87","last_name":"Hübschmann","first_name":"Verena","full_name":"Hübschmann, Verena"},{"last_name":"Korkut","first_name":"Medina","orcid":"0000-0003-4309-2251","full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"last_name":"Maya-Arteaga","first_name":"Juan Pablo","full_name":"Maya-Arteaga, Juan Pablo","id":"c815d433-1f5d-11f0-a875-dad18b1e5924"},{"first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"title":"Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids","status":"public","date_updated":"2026-08-12T08:45:16Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","intvolume":"        22","PlanS_conform":"1","publication_status":"published","publisher":"Springer Nature","corr_author":"1","type":"journal_article","citation":{"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>","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>.","short":"V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025).","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.","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>.","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."},"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"}],"scopus_import":"1","doi":"10.1186/s12974-025-03366-x","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/pink-skies/"}],"record":[{"status":"public","id":"20074","relation":"dissertation_contains"}]},"month":"04","file_date_updated":"2025-04-22T09:46:27Z","issue":"1","article_processing_charge":"Yes","isi":1,"language":[{"iso":"eng"}],"volume":22,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"quality_controlled":"1","ddc":["570"],"year":"2025"},{"title":"Human microglia impact neuronal development in retinal organoids","author":[{"full_name":"Hübschmann, Verena","first_name":"Verena","last_name":"Hübschmann","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-08-12T08:45:16Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2025-07-24T12:37:22Z","oa_version":"Published Version","_id":"20074","project":[{"name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"file":[{"creator":"vhuebsch","file_name":"PhD_Thesis_Schmied.zip","relation":"source_file","checksum":"d09f9984002353ad7442358394919bf3","date_created":"2025-07-30T08:47:53Z","file_size":43566093,"date_updated":"2025-07-30T08:47:53Z","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"20086"},{"access_level":"open_access","date_updated":"2025-07-30T09:29:09Z","content_type":"application/pdf","file_id":"20087","file_name":"PhD_Thesis_Schmied.pdf","creator":"vhuebsch","date_created":"2025-07-30T08:47:46Z","checksum":"4833690d7283c587f518ba98eeb2c946","file_size":13120922,"relation":"main_file"}],"date_published":"2025-07-24T00:00:00Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-060-2"]},"oa":1,"article_processing_charge":"No","month":"07","file_date_updated":"2025-07-30T09:29:09Z","page":"151","ddc":["570"],"year":"2025","language":[{"iso":"eng"}],"publication_status":"published","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","corr_author":"1","type":"dissertation","supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"has_accepted_license":"1","doi":"10.15479/AT-ISTA-20074","related_material":{"record":[{"relation":"part_of_dissertation","id":"11478","status":"public"},{"relation":"part_of_dissertation","id":"19593","status":"public"}]},"citation":{"apa":"Schmied, V. (2025). <i>Human microglia impact neuronal development in retinal organoids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>","mla":"Schmied, Verena. <i>Human Microglia Impact Neuronal Development in Retinal Organoids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>.","ista":"Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria.","chicago":"Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>.","ieee":"V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025.","ama":"Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>","short":"V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025."},"abstract":[{"lang":"eng","text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development."}]},{"status":"public","date_updated":"2026-08-12T08:44:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478.","article_type":"original","OA_place":"repository","department":[{"_id":"RoSe"}],"day":"23","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.16373"}],"author":[{"last_name":"Brooks","first_name":"Morris","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"}],"title":"Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling","oa":1,"external_id":{"arxiv":["2306.16373"]},"date_published":"2025-02-23T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"OA_type":"green","publication":"Probability and Mathematical Physics","date_created":"2025-03-09T23:01:28Z","oa_version":"Preprint","_id":"19372","language":[{"iso":"eng"}],"volume":6,"quality_controlled":"1","year":"2025","month":"02","page":"281-325","issue":"1","article_processing_charge":"No","citation":{"short":"M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325.","ama":"Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. 2025;6(1):281-325. doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>","ieee":"M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.","chicago":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2025. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>.","ista":"Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325.","apa":"Brooks, M., &#38; Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>","mla":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>."},"abstract":[{"text":"We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.","lang":"eng"}],"scopus_import":"1","doi":"10.2140/pmp.2025.6.281","intvolume":"         6","publication_status":"published","type":"journal_article","corr_author":"1","publisher":"Mathematical Sciences Publishers"},{"month":"04","file_date_updated":"2025-09-11T12:17:12Z","issue":"2","article_processing_charge":"Yes","isi":1,"language":[{"iso":"eng"}],"volume":21,"quality_controlled":"1","year":"2025","ddc":["000"],"has_accepted_license":"1","intvolume":"        21","PlanS_conform":"1","publication_status":"published","type":"journal_article","corr_author":"1","publisher":"EPI Sciences","citation":{"ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149.","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2025. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>.","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2. EPI Sciences, 2025.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025).","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. 2025;21(2). doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>."},"abstract":[{"lang":"eng","text":"Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata."}],"scopus_import":"1","doi":"10.46298/lmcs-21(2:2)2025","related_material":{"record":[{"status":"public","id":"13221","relation":"earlier_version"},{"relation":"dissertation_contains","id":"20147","status":"public"}]},"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","article_type":"original","OA_place":"publisher","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"day":"08","author":[{"last_name":"Boker","first_name":"Udi","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"title":"Safety and liveness of quantitative properties and automata","status":"public","date_updated":"2026-08-12T08:46:05Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Logical Methods in Computer Science","file":[{"access_level":"open_access","date_updated":"2025-09-11T12:17:12Z","content_type":"application/pdf","success":1,"file_id":"20343","file_name":"2307.06016.pdf","creator":"esarac","checksum":"0b4d477bd981379724c35a4de2c176e5","date_created":"2025-09-11T12:17:12Z","file_size":709584,"relation":"main_file"}],"date_created":"2025-09-11T12:17:52Z","article_number":"13149","oa_version":"Published Version","_id":"20342","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["001468887900001"],"arxiv":["2307.06016"]},"DOAJ_listed":"1","date_published":"2025-04-08T00:00:00Z","arxiv":1,"publication_identifier":{"eissn":["1860-5974"]},"OA_type":"gold"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T08:46:04Z","alternative_title":["ISTA Thesis"],"author":[{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E"}],"title":"A monitoring-oriented theory and classification of quantitative specifications","OA_place":"publisher","degree_awarded":"PhD","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"day":"07","ec_funded":1,"date_published":"2025-08-07T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"oa_version":"Published Version","date_created":"2025-08-07T15:57:57Z","project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"_id":"20147","file":[{"content_type":"application/x-zip-compressed","date_updated":"2025-09-10T08:19:51Z","access_level":"closed","file_id":"20200","creator":"esarac","file_name":"2025_Sarac_NaciEge_Thesis.zip","relation":"source_file","file_size":8884801,"date_created":"2025-08-21T09:40:28Z","checksum":"0f3015f1db36576a23d8d669afb60b41"},{"file_name":"2025_Sarac_NaciEge_Thesis.pdf","creator":"esarac","checksum":"332ed2fe61f580641664ec3f05d30f14","date_created":"2025-08-21T09:40:34Z","file_size":2955584,"relation":"main_file","access_level":"open_access","date_updated":"2025-08-21T09:40:34Z","content_type":"application/pdf","success":1,"file_id":"20201"}],"year":"2025","ddc":["000"],"language":[{"iso":"eng"}],"article_processing_charge":"No","month":"08","page":"149","file_date_updated":"2025-09-10T08:19:51Z","related_material":{"record":[{"id":"11775","relation":"part_of_dissertation","status":"public"},{"status":"deleted","relation":"part_of_dissertation","id":"13140"},{"status":"public","id":"19741","relation":"part_of_dissertation"},{"status":"deleted","relation":"part_of_dissertation","id":"19643"},{"status":"public","relation":"part_of_dissertation","id":"17634"},{"status":"public","relation":"part_of_dissertation","id":"13221"},{"status":"public","id":"9356","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"20342","status":"public"}]},"doi":"10.15479/AT-ISTA-20147","citation":{"apa":"Sarac, N. E. (2025). <i>A monitoring-oriented theory and classification of quantitative specifications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>","mla":"Sarac, Naci E. <i>A Monitoring-Oriented Theory and Classification of Quantitative Specifications</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>.","ama":"Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20147\">10.15479/AT-ISTA-20147</a>","short":"N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025.","chicago":"Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20147\">https://doi.org/10.15479/AT-ISTA-20147</a>.","ieee":"N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025.","ista":"Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria."},"abstract":[{"text":"Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n\r\n","lang":"eng"}],"doi_confirm":"1","publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink.  If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","publication_status":"published","supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","type":"dissertation","has_accepted_license":"1"},{"date_created":"2025-05-18T22:02:50Z","oa_version":"Published Version","_id":"19701","project":[{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"},{"grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"}],"pmid":1,"publication":"Annual Review of Biophysics","file":[{"access_level":"open_access","date_updated":"2025-05-19T07:55:51Z","content_type":"application/pdf","success":1,"file_id":"19710","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","creator":"dernst","date_created":"2025-05-19T07:55:51Z","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","file_size":317925,"relation":"main_file"}],"date_published":"2025-05-01T00:00:00Z","publication_identifier":{"eissn":["1936-1238"]},"OA_type":"hybrid","oa":1,"external_id":{"isi":["001488641500013"],"pmid":["39929539"]},"title":"Information processing in biochemical networks","author":[{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wolde","first_name":"Pieter Rein Ten","full_name":"Wolde, Pieter Rein Ten"}],"acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","OA_place":"publisher","article_type":"original","day":"01","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-08-12T09:25:42Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","publisher":"Annual Reviews","type":"journal_article","corr_author":"1","has_accepted_license":"1","intvolume":"        54","scopus_import":"1","doi":"10.1146/annurev-biophys-060524-102720","citation":{"short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274.","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual Review of Biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>."},"abstract":[{"text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","isi":1,"month":"05","file_date_updated":"2025-05-19T07:55:51Z","page":"249-274","quality_controlled":"1","ddc":["570"],"year":"2025","language":[{"iso":"eng"}],"volume":54},{"article_processing_charge":"Yes (via OA deal)","isi":1,"month":"06","file_date_updated":"2025-07-23T08:43:01Z","issue":"12","quality_controlled":"1","ddc":["570"],"year":"2025","language":[{"iso":"eng"}],"volume":152,"publication_status":"published","corr_author":"1","publisher":"Company of Biologists","type":"journal_article","has_accepted_license":"1","PlanS_conform":"1","intvolume":"       152","scopus_import":"1","doi":"10.1242/dev.204261","citation":{"short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>.","ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. Company of Biologists, 2025.","apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>."},"abstract":[{"lang":"eng","text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations."}],"title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","author":[{"orcid":"0000-0002-2853-8051","full_name":"Moriyama, Yuuta","last_name":"Moriyama","first_name":"Yuuta","id":"addc9b8c-67a0-11f0-b374-a2e094825470"},{"full_name":"Mitsui, Toshiyuki","first_name":"Toshiyuki","last_name":"Mitsui"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","article_type":"original","OA_place":"publisher","day":"27","department":[{"_id":"CaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-08-12T10:01:31Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2025-07-21T08:10:32Z","article_number":"dev204261","oa_version":"Published Version","_id":"20048","pmid":1,"publication":"Development","file":[{"relation":"main_file","date_created":"2025-07-23T08:43:01Z","checksum":"808d8aa28df79d23fb661838d1fdc1be","file_size":25935563,"creator":"dernst","file_name":"2025_Development_Moriyama.pdf","file_id":"20070","date_updated":"2025-07-23T08:43:01Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"date_published":"2025-06-27T00:00:00Z","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"OA_type":"hybrid","oa":1,"external_id":{"isi":["001525252300001"],"pmid":["40576478"]}},{"file_date_updated":"2026-02-24T07:56:34Z","page":"1677-1691","month":"10","article_processing_charge":"Yes","volume":12,"language":[{"iso":"eng"}],"ddc":["510"],"year":"2025","quality_controlled":"1","PlanS_conform":"1","intvolume":"        12","has_accepted_license":"1","type":"journal_article","corr_author":"1","publisher":"Ecole Polytechnique","supplementarymaterial":"no","publication_status":"published","abstract":[{"text":"The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given","lang":"eng"},{"lang":"fre","text":" Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques."}],"citation":{"ama":"Browning TD, Chan S. Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2025;12:1677-1691. doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>","short":"T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691.","chicago":"Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2025. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>.","ieee":"T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025.","ista":"Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.","apa":"Browning, T. D., &#38; Chan, S. (2025). Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>","mla":"Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>."},"doi":"10.5802/jep.320","scopus_import":"1","das_tickbox":"0","department":[{"_id":"TiBr"}],"day":"21","acknowledgement":"While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278).","OA_place":"publisher","article_type":"original","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","first_name":"Timothy D","last_name":"Browning"},{"last_name":"Chan","first_name":"Yik Tung","orcid":"0000-0001-8467-4106","full_name":"Chan, Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1"}],"title":"Solubility of a resultant equation and applications","date_updated":"2026-08-12T11:17:50Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_name":"2025_JEP_Browning.pdf","relation":"main_file","file_size":1003689,"checksum":"828577ea48ac6109d3e9dd1aeddd45c4","date_created":"2026-02-24T07:56:34Z","success":1,"content_type":"application/pdf","date_updated":"2026-02-24T07:56:34Z","access_level":"open_access","file_id":"21356"}],"publication":"Journal de l'Ecole Polytechnique - Mathematiques","_id":"21343","project":[{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"date_created":"2026-02-22T23:01:36Z","oa_version":"Published Version","oa":1,"researchdata_availability":"no","external_id":{"arxiv":["2411.09264"]},"arxiv":1,"OA_type":"gold","publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"DOAJ_listed":"1","date_published":"2025-10-21T00:00:00Z"},{"file":[{"file_id":"20281","access_level":"open_access","date_updated":"2025-09-03T06:44:44Z","success":1,"content_type":"application/pdf","date_created":"2025-09-03T06:44:44Z","checksum":"89352f1f7e8d2b367ae5f4e9bf9eb1f5","file_size":2484757,"relation":"main_file","file_name":"2025_SelectaMathematica_Browning.pdf","creator":"dernst"}],"publication":"Selecta Mathematica New Series","_id":"20249","project":[{"call_identifier":"FWF","name":"New frontiers of the Manin conjecture","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","grant_number":"P32428"},{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"date_created":"2025-08-31T22:01:31Z","article_number":"81","oa_version":"Published Version","oa":1,"researchdata_availability":"yes","external_id":{"isi":["001552779800001"],"arxiv":["2407.16315"]},"arxiv":1,"publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"OA_type":"hybrid","date_published":"2025-09-01T00:00:00Z","das_tickbox":"1","department":[{"_id":"TiBr"}],"day":"01","acknowledgement":"The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","article_type":"original","OA_place":"publisher","title":"Integral points on cubic surfaces: heuristics and numerics","author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian Alexander","last_name":"Wilsch","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425"}],"date_updated":"2026-08-12T12:15:32Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        31","PlanS_conform":"1","dataavailabilitystatement":"The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page.","has_accepted_license":"1","publisher":"Springer Nature","corr_author":"1","type":"journal_article","supplementarymaterial":"yes","publication_status":"published","abstract":[{"text":"We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.","lang":"eng"}],"citation":{"apa":"Browning, T. D., &#38; Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>","mla":"Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4, 81, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>.","ista":"Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.","ieee":"T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4. Springer Nature, 2025.","chicago":"Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>.","short":"T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).","ama":"Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. 2025;31(4). doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>"},"doi":"10.1007/s00029-025-01074-1","related_material":{"link":[{"relation":"software","url":"https://github.com/fwilsch/cubicpts"}],"record":[{"status":"public","id":"22234","relation":"research_data"}]},"scopus_import":"1","file_date_updated":"2025-09-03T06:44:44Z","issue":"4","month":"09","isi":1,"article_processing_charge":"Yes (via OA deal)","volume":31,"language":[{"iso":"eng"}],"year":"2025","ddc":["500"],"quality_controlled":"1"},{"intvolume":"       638","has_accepted_license":"1","type":"journal_article","publisher":"Springer Nature","corr_author":"1","publication_status":"published","abstract":[{"text":"When two insulating, neutral materials are contacted and separated, they exchange electrical charge1. Experiments have long suggested that this ‘contact electrification’ is transitive, with different materials ordering into ‘triboelectric series’ based on the sign of charge acquired2. At the same time, the effect is plagued by unpredictability, preventing consensus on the mechanism and casting doubt on the rhyme and reason that series imply3. Here we expose an unanticipated connection between the unpredictability and order in contact electrification: nominally identical materials initially exchange charge randomly and intransitively, but—over repeated experiments—order into triboelectric series. We find that this evolution is driven by the act of contact itself—samples with more contacts in their history charge negatively to ones with fewer contacts. Capturing this ‘contact bias’ in a minimal model, we recreate both the initial randomness and ultimate order in numerical simulations and use it experimentally to force the appearance of a triboelectric series of our choosing. With a set of surface-sensitive techniques to search for the underlying alterations contact creates, we only find evidence of nanoscale morphological changes, pointing to a mechanism strongly coupled with mechanics. Our results highlight the centrality of contact history in contact electrification and suggest that focusing on the unpredictability that has long plagued the effect may hold the key to understanding it.","lang":"eng"}],"citation":{"short":"J.C.A. Sobarzo Ponce, F. Pertl, D. Balazs, T. Costanzo, M. Sauer, A. Foelske, M. Ostermann, C.M. Pichler, Y. Wang, Y. Nagata, M. Bonn, S.R. Waitukaitis, Nature 638 (2025).","ama":"Sobarzo Ponce JCA, Pertl F, Balazs D, et al. Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. 2025;638(8051). doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>","chicago":"Sobarzo Ponce, Juan Carlos A, Felix Pertl, Daniel Balazs, Tommaso Costanzo, Markus Sauer, Annette Foelske, Markus Ostermann, et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>.","ista":"Sobarzo Ponce JCA, Pertl F, Balazs D, Costanzo T, Sauer M, Foelske A, Ostermann M, Pichler CM, Wang Y, Nagata Y, Bonn M, Waitukaitis SR. 2025. Spontaneous ordering of identical materials into a triboelectric series. Nature. 638(8051), 664–669.","ieee":"J. C. A. Sobarzo Ponce <i>et al.</i>, “Spontaneous ordering of identical materials into a triboelectric series,” <i>Nature</i>, vol. 638, no. 8051. Springer Nature, 2025.","apa":"Sobarzo Ponce, J. C. A., Pertl, F., Balazs, D., Costanzo, T., Sauer, M., Foelske, A., … Waitukaitis, S. R. (2025). Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>","mla":"Sobarzo Ponce, Juan Carlos A., et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>, vol. 638, no. 8051, 664–669, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>."},"related_material":{"record":[{"status":"public","id":"20203","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"22684","status":"for_moderation"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/","description":"News on ISTA website"}]},"doi":"10.1038/s41586-024-08530-6","scopus_import":"1","issue":"8051","file_date_updated":"2025-03-04T10:05:18Z","month":"02","isi":1,"article_processing_charge":"Yes (via OA deal)","volume":638,"language":[{"iso":"eng"}],"year":"2025","ddc":["530"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"file":[{"success":1,"content_type":"application/pdf","date_updated":"2025-03-04T10:05:18Z","access_level":"open_access","file_id":"19289","creator":"dernst","file_name":"2025_Nature_Sobarzo.pdf","relation":"main_file","file_size":3807415,"date_created":"2025-03-04T10:05:18Z","checksum":"fecf302274dd3218d3e7dd22f39a6c0c"}],"publication":"Nature","pmid":1,"project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"_id":"19278","oa_version":"Published Version","article_number":"664-669","date_created":"2025-03-02T23:01:52Z","external_id":{"isi":["001428076100015"],"pmid":["39972227"]},"oa":1,"OA_type":"hybrid","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_published":"2025-02-20T00:00:00Z","department":[{"_id":"ScWa"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"day":"20","ec_funded":1,"OA_place":"publisher","article_type":"original","acknowledgement":"This project has received financing from the European Research Council grant agreement no. 949120 under the European Union’s Horizon 2020 research and innovation programme. The Analytical Instrumentation Center of the TU Wien acknowledges support by the FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility, Electron Microscopy Facility and Lab Support Facility. We thank J. Garcia-Suarez and G. Anciaux for the suggestion to look into the roughness power spectral density. We thank I.-M. Strugaru for help with testing the device for Young’s modulus measurements. Open access funding provided by Institute of Science and Technology (IST Austria).","author":[{"id":"4B807D68-AE37-11E9-AC72-31CAE5697425","full_name":"Sobarzo Ponce, Juan Carlos A","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce"},{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix","last_name":"Pertl","full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"last_name":"Sauer","first_name":"Markus","full_name":"Sauer, Markus"},{"last_name":"Foelske","first_name":"Annette","full_name":"Foelske, Annette"},{"last_name":"Ostermann","first_name":"Markus","full_name":"Ostermann, Markus"},{"first_name":"Christian M.","last_name":"Pichler","full_name":"Pichler, Christian M."},{"last_name":"Wang","first_name":"Yongkang","full_name":"Wang, Yongkang"},{"full_name":"Nagata, Yuki","first_name":"Yuki","last_name":"Nagata"},{"first_name":"Mischa","last_name":"Bonn","full_name":"Bonn, Mischa"},{"first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"title":"Spontaneous ordering of identical materials into a triboelectric series","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T13:08:54Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"file":[{"file_name":"2025_PhysReviewLetters_Pertl.pdf","creator":"dernst","date_created":"2025-10-23T09:32:31Z","checksum":"7e45e89b8db0b7f01e63185c68e4b0f9","file_size":1692251,"relation":"main_file","access_level":"open_access","date_updated":"2025-10-23T09:32:31Z","success":1,"content_type":"application/pdf","file_id":"20522"}],"publication":"Physical Review Letters","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020"}],"_id":"20481","oa_version":"Published Version","article_number":"146202","date_created":"2025-10-16T13:13:29Z","external_id":{"isi":["001587263900003"],"arxiv":["2502.12718"]},"oa":1,"OA_type":"hybrid","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"date_published":"2025-09-30T00:00:00Z","department":[{"_id":"ScWa"}],"day":"30","ec_funded":1,"OA_place":"publisher","article_type":"original","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the Nanofabrication Facility and Lab Support Facility.","title":"No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces","author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794","first_name":"Felix","last_name":"Pertl"},{"last_name":"Lenton","first_name":"Isaac C","full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"full_name":"Cramer, Tobias","last_name":"Cramer","first_name":"Tobias"},{"last_name":"Waitukaitis","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T13:08:54Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","intvolume":"       135","has_accepted_license":"1","publisher":"American Physical Society","corr_author":"1","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"Kelvin probe force microscopy (KPFM) is widely used in stationary and dynamic studies of contact electrification. An obvious question that connects these two has been overlooked: when are charge dynamics too fast for stationary studies to be meaningful? Using a rapid transfer system to quickly perform KPFM after contact, we find the dynamics are too fast in all but the best insulators. Our data further suggest that dynamics are caused by bulk as opposed to surface conductivity, and that charge-transfer heterogeneity is less prevalent than previously suggested."}],"citation":{"apa":"Pertl, F., Lenton, I. C., Cramer, T., &#38; Waitukaitis, S. R. (2025). No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>","mla":"Pertl, Felix, et al. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>, vol. 135, no. 14, 146202, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>.","chicago":"Pertl, Felix, Isaac C Lenton, Tobias Cramer, and Scott R Waitukaitis. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>.","ista":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. 2025. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. Physical Review Letters. 135(14), 146202.","ieee":"F. Pertl, I. C. Lenton, T. Cramer, and S. R. Waitukaitis, “No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces,” <i>Physical Review Letters</i>, vol. 135, no. 14. American Physical Society, 2025.","short":"F. Pertl, I.C. Lenton, T. Cramer, S.R. Waitukaitis, Physical Review Letters 135 (2025).","ama":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. 2025;135(14). doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"20523"},{"status":"for_moderation","relation":"dissertation_contains","id":"22684"}]},"doi":"10.1103/lcsm-xxty","scopus_import":"1","issue":"14","file_date_updated":"2025-10-23T09:32:31Z","month":"09","isi":1,"article_processing_charge":"Yes (via OA deal)","volume":135,"language":[{"iso":"eng"}],"year":"2025","ddc":["530"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-08-12T13:57:57Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"full_name":"Jaeger, Eliza C.B.","last_name":"Jaeger","first_name":"Eliza C.B."},{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","first_name":"David","last_name":"Vijatovic","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941"},{"last_name":"Deryckere","first_name":"Astrid","full_name":"Deryckere, Astrid"},{"last_name":"Zorin","first_name":"Nikol","full_name":"Zorin, Nikol"},{"last_name":"Nguyen","first_name":"Akemi L.","full_name":"Nguyen, Akemi L."},{"id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05","orcid":"0009-0002-3999-3735","full_name":"Ivanian, Georgiy","first_name":"Georgiy","last_name":"Ivanian"},{"last_name":"Woych","first_name":"Jamie","full_name":"Woych, Jamie"},{"last_name":"Arnold","first_name":"Rebecca C","full_name":"Arnold, Rebecca C","id":"d6cce458-14c9-11ed-a755-c1c8fc6fde6f"},{"full_name":"Ortega Gurrola, Alonso","first_name":"Alonso","last_name":"Ortega Gurrola"},{"full_name":"Shvartsman, Arik","last_name":"Shvartsman","first_name":"Arik"},{"last_name":"Barbieri","first_name":"Francesca","full_name":"Barbieri, Francesca","id":"a9492887-8972-11ed-ae7b-bfae10998254"},{"id":"85dd99f2-15b2-11ec-abd3-d1ae4d57f3b5","first_name":"Florina-Alexandra","last_name":"Toma","full_name":"Toma, Florina-Alexandra"},{"full_name":"Gorbsky, Gary J.","last_name":"Gorbsky","first_name":"Gary J."},{"full_name":"Horb, Marko E.","last_name":"Horb","first_name":"Marko E."},{"full_name":"Cline, Hollis T.","last_name":"Cline","first_name":"Hollis T."},{"full_name":"Shay, Timothy F.","first_name":"Timothy F.","last_name":"Shay"},{"last_name":"Kelley","first_name":"Darcy B.","full_name":"Kelley, Darcy B."},{"last_name":"Yamaguchi","first_name":"Ayako","full_name":"Yamaguchi, Ayako"},{"full_name":"Shein-Idelson, Mark","last_name":"Shein-Idelson","first_name":"Mark"},{"full_name":"Tosches, Maria Antonietta","last_name":"Tosches","first_name":"Maria Antonietta"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"}],"title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"day":"10","acknowledgement":"We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).","article_type":"original","OA_place":"publisher","OA_type":"hybrid","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_published":"2025-03-10T00:00:00Z","oa":1,"external_id":{"pmid":["39603234"],"isi":["001444798600001"]},"_id":"15016","pmid":1,"project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis"},{"grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","grant_number":"F7814","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e"}],"date_created":"2024-02-20T09:20:32Z","oa_version":"Published Version","file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2025-06-04T05:43:27Z","file_id":"19790","file_name":"2025_DevelopmentalCell_Jaeger.pdf","creator":"dernst","file_size":11936258,"date_created":"2025-06-04T05:43:27Z","checksum":"a83a4cb58f5941096d3ad91ca0172594","relation":"main_file"}],"publication":"Developmental Cell","year":"2025","ddc":["570"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"quality_controlled":"1","volume":60,"language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-06-04T05:43:27Z","issue":"5","page":"794-812.e6","month":"03","doi":"10.1016/j.devcel.2024.10.025","related_material":{"record":[{"id":"22667","relation":"dissertation_contains","status":"for_moderation"}]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution."}],"citation":{"apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>, vol. 60, no. 5, Elsevier, 2025, p. 794–812.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>.","ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. 2025;60(5):794-812.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6.","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>Developmental Cell</i>, vol. 60, no. 5. Elsevier, p. 794–812.e6, 2025.","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>."},"corr_author":"1","type":"journal_article","publisher":"Elsevier","publication_status":"published","intvolume":"        60","has_accepted_license":"1"},{"department":[{"_id":"JePa"}],"day":"18","acknowledgement":"Living Architecture is Funded by the EU Horizon 2020 Future Emerging Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6 collaborating institutions—Newcastle University, University of Trento, University of the West of England, Spanish National Research Council, Explora Biotech and Liquifer Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE) project is funded by an EU Innovation Award for the development of a bio-digital ‘brick’ prototype, a collaboration between Newcastle University, Translating Nature, and the University of the West of England (2019–2021) under EU Grant Agreement No. 851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy) is Funded by the European Union under Grant Agreement Number 101114746, which is a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton (UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish National Research Council (Spain), and Associated Partners, the University of the West of England (UK) and University of Southampton (UK). Mi-Hy is also supported through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL).","article_type":"original","OA_place":"publisher","title":"Roadmap for animate matter","author":[{"last_name":"Volpe","first_name":"Giorgio","full_name":"Volpe, Giorgio"},{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"first_name":"Maria","last_name":"Guix","full_name":"Guix, Maria"},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"first_name":"Nicolas","last_name":"Martin","full_name":"Martin, Nicolas"},{"first_name":"Laura","last_name":"Alvarez","full_name":"Alvarez, Laura"},{"last_name":"Simmchen","first_name":"Juliane","full_name":"Simmchen, Juliane"},{"full_name":"Leonardo, Roberto Di","last_name":"Leonardo","first_name":"Roberto Di"},{"full_name":"Pellicciotta, Nicola","last_name":"Pellicciotta","first_name":"Nicola"},{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","last_name":"Martinet","first_name":"Quentin"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Ng, Wai Kit","last_name":"Ng","first_name":"Wai Kit"},{"last_name":"Saxena","first_name":"Dhruv","full_name":"Saxena, Dhruv"},{"full_name":"Sapienza, Riccardo","first_name":"Riccardo","last_name":"Sapienza"},{"full_name":"Nadine, Sara","last_name":"Nadine","first_name":"Sara"},{"first_name":"João F.","last_name":"Mano","full_name":"Mano, João F."},{"full_name":"Mahdavi, Reza","last_name":"Mahdavi","first_name":"Reza"},{"first_name":"Caroline","last_name":"Beck Adiels","full_name":"Beck Adiels, Caroline"},{"full_name":"Forth, Joe","last_name":"Forth","first_name":"Joe"},{"last_name":"Santangelo","first_name":"Christian","full_name":"Santangelo, Christian"},{"last_name":"Palagi","first_name":"Stefano","full_name":"Palagi, Stefano"},{"full_name":"Seok, Ji Min","last_name":"Seok","first_name":"Ji Min"},{"last_name":"Webster-Wood","first_name":"Victoria A.","full_name":"Webster-Wood, Victoria A."},{"first_name":"Shuhong","last_name":"Wang","full_name":"Wang, Shuhong"},{"first_name":"Lining","last_name":"Yao","full_name":"Yao, Lining"},{"last_name":"Aghakhani","first_name":"Amirreza","full_name":"Aghakhani, Amirreza"},{"full_name":"Barois, Thomas","last_name":"Barois","first_name":"Thomas"},{"last_name":"Kellay","first_name":"Hamid","full_name":"Kellay, Hamid"},{"first_name":"Corentin","last_name":"Coulais","full_name":"Coulais, Corentin"},{"full_name":"Van Hecke, Martin","first_name":"Martin","last_name":"Van Hecke"},{"full_name":"Pierce, Christopher J.","first_name":"Christopher J.","last_name":"Pierce"},{"full_name":"Wang, Tianyu","first_name":"Tianyu","last_name":"Wang"},{"full_name":"Chong, Baxi","first_name":"Baxi","last_name":"Chong"},{"full_name":"Goldman, Daniel I.","first_name":"Daniel I.","last_name":"Goldman"},{"full_name":"Reina, Andreagiovanni","last_name":"Reina","first_name":"Andreagiovanni"},{"last_name":"Trianni","first_name":"Vito","full_name":"Trianni, Vito"},{"full_name":"Volpe, Giovanni","first_name":"Giovanni","last_name":"Volpe"},{"full_name":"Beckett, Richard","last_name":"Beckett","first_name":"Richard"},{"full_name":"Nair, Sean P.","first_name":"Sean P.","last_name":"Nair"},{"full_name":"Armstrong, Rachel","last_name":"Armstrong","first_name":"Rachel"}],"date_updated":"2026-08-12T14:00:12Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2025-09-02T07:22:48Z","checksum":"7309274f78bed785b158bd290337f456","file_size":8997829,"relation":"main_file","file_name":"2025_CondensedMatter_Volpe.pdf","creator":"dernst","file_id":"20271","access_level":"open_access","date_updated":"2025-09-02T07:22:48Z","success":1,"content_type":"application/pdf"}],"publication":"Journal of Physics: Condensed Matter","_id":"20218","date_created":"2025-08-24T22:01:30Z","oa_version":"Published Version","article_number":"333501","oa":1,"external_id":{"arxiv":["2407.10623"],"isi":["001550090200001"]},"arxiv":1,"OA_type":"hybrid","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"date_published":"2025-08-18T00:00:00Z","file_date_updated":"2025-09-02T07:22:48Z","issue":"33","month":"08","isi":1,"article_processing_charge":"Yes (in subscription journal)","volume":37,"language":[{"iso":"eng"}],"ddc":["530"],"year":"2025","quality_controlled":"1","PlanS_conform":"1","intvolume":"        37","has_accepted_license":"1","type":"journal_article","publisher":"IOP Publishing","publication_status":"published","abstract":[{"lang":"eng","text":"Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner."}],"citation":{"ama":"Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. 2025;37(33). doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>","short":"G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J. Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng, D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth, C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani, T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong, D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong, Journal of Physics: Condensed Matter 37 (2025).","ista":"Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J, Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal of Physics: Condensed Matter. 37(33), 333501.","chicago":"Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>.","ieee":"G. Volpe <i>et al.</i>, “Roadmap for animate matter,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33. IOP Publishing, 2025.","mla":"Volpe, Giorgio, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>.","apa":"Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>"},"doi":"10.1088/1361-648X/adebd3","scopus_import":"1"},{"article_type":"original","OA_place":"publisher","acknowledgement":"We thank Kimberly A. Modic for her support and discussions regarding the technique in the context of a project indirectly related to, but distinct from, the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific discussions not directly related to this study, but whose insights proved helpful. We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain for informal discussions on various aspects of the technique, and to Naoya Iwahara for his thoughtful and constructive feedback. The experimental curve shown in figures 3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for granting access to the laboratory facilities. Je Geun Park provided the crystal used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge. Institutional support from the Institute of Science and Technology Austria (ISTA) is also gratefully acknowledged.","department":[{"_id":"KiMo"}],"day":"06","author":[{"first_name":"Hamza","last_name":"Farooq","full_name":"Farooq, Hamza"},{"first_name":"Muhammad","last_name":"Nauman","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"}],"title":"Non-linear magnetotropic susceptibility in FePS3","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T14:00:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Physics: Condensed Matter","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2025-10-13T06:34:15Z","file_id":"20458","file_name":"2025_JourPhysicsCondMatter_Farooq.pdf","creator":"dernst","file_size":1709516,"checksum":"b182856a5a655496e149afa49ec464f3","date_created":"2025-10-13T06:34:15Z","relation":"main_file"}],"oa_version":"Published Version","article_number":"405801","date_created":"2025-10-12T22:01:26Z","pmid":1,"_id":"20453","external_id":{"isi":["001585824100001"],"pmid":["40967257"]},"oa":1,"date_published":"2025-10-06T00:00:00Z","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"OA_type":"hybrid","month":"10","issue":"40","file_date_updated":"2025-10-13T06:34:15Z","article_processing_charge":"Yes (via OA deal)","isi":1,"language":[{"iso":"eng"}],"volume":37,"quality_controlled":"1","year":"2025","ddc":["530"],"has_accepted_license":"1","intvolume":"        37","PlanS_conform":"1","publication_status":"published","publisher":"IOP Publishing","type":"journal_article","corr_author":"1","citation":{"ama":"Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. 2025;37(40). doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>","short":"H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).","chicago":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>.","ieee":"H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40. IOP Publishing, 2025.","ista":"Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. 37(40), 405801.","apa":"Farooq, H., &#38; Nauman, M. (2025). Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>","mla":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40, 405801, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>."},"abstract":[{"text":"Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work.","lang":"eng"}],"scopus_import":"1","doi":"10.1088/1361-648X/ae0913"},{"date_created":"2025-08-24T22:01:30Z","oa_version":"None","article_number":"20250202","_id":"20219","pmid":1,"publication":"Journal of the Royal Society Interface","date_published":"2025-08-13T00:00:00Z","OA_type":"closed access","publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"external_id":{"isi":["001548084900001"],"pmid":["40799050"]},"author":[{"full_name":"Ayalon, Oran","first_name":"Oran","last_name":"Ayalon"},{"first_name":"Harikrishnan","last_name":"Rajendran","full_name":"Rajendran, Harikrishnan","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416"}],"title":"Interplay of asexual and sexual reproduction in bifunctional insects","acknowledgement":"We acknowledge Prof. Uri Alon for introducing us to the topic of systems biology during the graduate course at the Weizmann Institute of Science, whose insights and teachings have greatly inspired this work.","article_type":"original","day":"13","department":[{"_id":"SyCr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2026-08-12T14:09:20Z","publication_status":"published","type":"journal_article","publisher":"Royal Society","corr_author":"1","intvolume":"        22","scopus_import":"1","doi":"10.1098/rsif.2025.0202","citation":{"ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.","ieee":"O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229. Royal Society, 2025.","chicago":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>.","short":"O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).","ama":"Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. 2025;22(229). doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>","apa":"Ayalon, O., &#38; Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>","mla":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229, 20250202, Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>."},"abstract":[{"text":"Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.","lang":"eng"}],"article_processing_charge":"No","isi":1,"month":"08","issue":"229","quality_controlled":"1","year":"2025","language":[{"iso":"eng"}],"volume":22},{"page":"170","file_date_updated":"2026-03-26T23:30:03Z","month":"03","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2025","ddc":["570","576"],"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","corr_author":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","abstract":[{"lang":"eng","text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. "}],"citation":{"ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.","mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. 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