--- APC_amount: 3948 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '19593' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: We thank the scientific service units at ISTA, specifically the Lab Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the Imaging and Optics Facility (IOF). We thank all members of the Siegert group and Marco Benevento for their constant feedback on the project and comments on the manuscript. A special thanks to Rouven Schulz for input on statistical analysis and sharing R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and Florianne Schoot Uiterkamp for their support in cell culture. This research was supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). article_number: '98' article_processing_charge: Yes article_type: original author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann - first_name: Medina full_name: Korkut, Medina id: 4B51CE74-F248-11E8-B48F-1D18A9856A87 last_name: Korkut orcid: 0000-0003-4309-2251 - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Juan Pablo full_name: Maya-Arteaga, Juan Pablo id: c815d433-1f5d-11f0-a875-dad18b1e5924 last_name: Maya-Arteaga - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: 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. Journal of Neuroinflammation. 2025;22(1). doi:10.1186/s12974-025-03366-x apa: Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., & Siegert, S. (2025). Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. Springer Nature. https://doi.org/10.1186/s12974-025-03366-x 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.” Journal of Neuroinflammation. Springer Nature, 2025. https://doi.org/10.1186/s12974-025-03366-x. 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,” Journal of Neuroinflammation, vol. 22, no. 1. Springer Nature, 2025. 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. mla: Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation, vol. 22, no. 1, 98, Springer Nature, 2025, doi:10.1186/s12974-025-03366-x. short: V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025). corr_author: '1' date_created: 2025-04-20T22:01:28Z date_published: 2025-04-03T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '03' ddc: - '570' department: - _id: SaSi doi: 10.1186/s12974-025-03366-x external_id: isi: - '001459311800002' pmid: - '40181459' file: - access_level: open_access checksum: dcc355c21ab713e45fda5c61b5fa5299 content_type: application/pdf creator: dernst date_created: 2025-04-22T09:46:27Z date_updated: 2025-04-22T09:46:27Z file_id: '19607' file_name: 2025_JourNeuroinflammation_Schmied.pdf file_size: 4482167 relation: main_file success: 1 file_date_updated: 2025-04-22T09:46:27Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version 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 publication: Journal of Neuroinflammation publication_identifier: eissn: - 1742-2094 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/pink-skies/ record: - id: '20074' relation: dissertation_contains status: public scopus_import: '1' status: public title: Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2025' ... --- OA_place: publisher _id: '20074' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann citation: ama: Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074 apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074 chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074. ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025. ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074. short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-24T12:37:22Z date_published: 2025-07-24T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20074 doi_confirm: '1' file: - access_level: closed checksum: d09f9984002353ad7442358394919bf3 content_type: application/x-zip-compressed creator: vhuebsch date_created: 2025-07-30T08:47:53Z date_updated: 2025-07-30T08:47:53Z file_id: '20086' file_name: PhD_Thesis_Schmied.zip file_size: 43566093 relation: source_file - access_level: open_access checksum: 4833690d7283c587f518ba98eeb2c946 content_type: application/pdf creator: vhuebsch date_created: 2025-07-30T08:47:46Z date_updated: 2025-07-30T09:29:09Z file_id: '20087' file_name: PhD_Thesis_Schmied.pdf file_size: 13120922 relation: main_file file_date_updated: 2025-07-30T09:29:09Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '151' project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation publication_identifier: isbn: - 978-3-99078-060-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11478' relation: part_of_dissertation status: public - id: '19593' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Human microglia impact neuronal development in retinal organoids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '19372' abstract: - lang: eng 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. acknowledgement: M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas citation: ama: Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 2025;6(1):281-325. doi:10.2140/pmp.2025.6.281 apa: Brooks, M., & Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2025.6.281 chicago: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/pmp.2025.6.281. ieee: M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” Probability and Mathematical Physics, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025. 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. mla: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:10.2140/pmp.2025.6.281. short: M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325. corr_author: '1' date_created: 2025-03-09T23:01:28Z date_published: 2025-02-23T00:00:00Z date_updated: 2026-08-12T08:44:53Z day: '23' department: - _id: RoSe doi: 10.2140/pmp.2025.6.281 external_id: arxiv: - '2306.16373' intvolume: ' 6' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.16373 month: '02' oa: 1 oa_version: Preprint page: 281-325 publication: Probability and Mathematical Physics publication_identifier: eissn: - 2690-1005 issn: - 2690-0998 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20342' 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. 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_number: '13149' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 2025;21(2). doi:10.46298/lmcs-21(2:2)2025 apa: Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025 chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025. ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” Logical Methods in Computer Science, vol. 21, no. 2. EPI Sciences, 2025. 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. mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:10.46298/lmcs-21(2:2)2025. short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025). corr_author: '1' date_created: 2025-09-11T12:17:52Z date_published: 2025-04-08T00:00:00Z date_updated: 2026-08-12T08:46:05Z day: '08' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.46298/lmcs-21(2:2)2025 ec_funded: 1 external_id: arxiv: - '2307.06016' isi: - '001468887900001' file: - access_level: open_access checksum: 0b4d477bd981379724c35a4de2c176e5 content_type: application/pdf creator: esarac date_created: 2025-09-11T12:17:12Z date_updated: 2025-09-11T12:17:12Z file_id: '20343' file_name: 2307.06016.pdf file_size: 709584 relation: main_file success: 1 file_date_updated: 2025-09-11T12:17:12Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Logical Methods in Computer Science publication_identifier: eissn: - 1860-5974 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '13221' relation: earlier_version status: public - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: Safety and liveness of quantitative properties and automata tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2025' ... --- OA_place: publisher _id: '20147' abstract: - lang: eng 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" 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:10.15479/AT-ISTA-20147 apa: Sarac, N. E. (2025). A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20147 chicago: Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20147. 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. mla: Sarac, Naci E. A Monitoring-Oriented Theory and Classification of Quantitative Specifications. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20147. short: N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-07T15:57:57Z date_published: 2025-08-07T00:00:00Z date_updated: 2026-08-12T08:46:04Z day: '07' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ToHe doi: 10.15479/AT-ISTA-20147 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 0f3015f1db36576a23d8d669afb60b41 content_type: application/x-zip-compressed creator: esarac date_created: 2025-08-21T09:40:28Z date_updated: 2025-09-10T08:19:51Z file_id: '20200' file_name: 2025_Sarac_NaciEge_Thesis.zip file_size: 8884801 relation: source_file - access_level: open_access checksum: 332ed2fe61f580641664ec3f05d30f14 content_type: application/pdf creator: esarac date_created: 2025-08-21T09:40:34Z date_updated: 2025-08-21T09:40:34Z file_id: '20201' file_name: 2025_Sarac_NaciEge_Thesis.pdf file_size: 2955584 relation: main_file success: 1 file_date_updated: 2025-09-10T08:19:51Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '149' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria 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." related_material: record: - id: '11775' relation: part_of_dissertation status: public - id: '13140' relation: part_of_dissertation status: deleted - id: '19741' relation: part_of_dissertation status: public - id: '19643' relation: part_of_dissertation status: deleted - id: '17634' relation: part_of_dissertation status: public - id: '13221' relation: part_of_dissertation status: public - id: '9356' relation: part_of_dissertation status: public - id: '20342' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: A monitoring-oriented theory and classification of quantitative specifications tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19701' abstract: - lang: eng 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.' 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). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Pieter Rein Ten full_name: Wolde, Pieter Rein Ten last_name: Wolde citation: ama: Tkačik G, Wolde PRT. Information processing in biochemical networks. Annual Review of Biophysics. 2025;54:249-274. doi:10.1146/annurev-biophys-060524-102720 apa: Tkačik, G., & Wolde, P. R. T. (2025). Information processing in biochemical networks. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-060524-102720 chicago: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-biophys-060524-102720. ieee: G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” Annual Review of Biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025. ista: Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274. mla: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:10.1146/annurev-biophys-060524-102720. short: G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274. corr_author: '1' date_created: 2025-05-18T22:02:50Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-08-12T09:25:42Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1146/annurev-biophys-060524-102720 external_id: isi: - '001488641500013' pmid: - '39929539' file: - access_level: open_access checksum: 9ab623b2bc45dcd5fdd2c9577ea8ae9f content_type: application/pdf creator: dernst date_created: 2025-05-19T07:55:51Z date_updated: 2025-05-19T07:55:51Z file_id: '19710' file_name: 2025_AnnualReviewBiophysics_Tkacik.pdf file_size: 317925 relation: main_file success: 1 file_date_updated: 2025-05-19T07:55:51Z has_accepted_license: '1' intvolume: ' 54' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 249-274 pmid: 1 project: - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' 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 publication: Annual Review of Biophysics publication_identifier: eissn: - 1936-1238 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Information processing in biochemical networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20048' 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.' 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_number: dev204261 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yuuta full_name: Moriyama, Yuuta id: addc9b8c-67a0-11f0-b374-a2e094825470 last_name: Moriyama orcid: 0000-0002-2853-8051 - first_name: Toshiyuki full_name: Mitsui, Toshiyuki last_name: Mitsui - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 2025;152(12). doi:10.1242/dev.204261 apa: Moriyama, Y., Mitsui, T., & Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.204261 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.” Development. Company of Biologists, 2025. https://doi.org/10.1242/dev.204261. 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,” Development, vol. 152, no. 12. Company of Biologists, 2025. 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. mla: Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:10.1242/dev.204261. short: Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025). corr_author: '1' date_created: 2025-07-21T08:10:32Z date_published: 2025-06-27T00:00:00Z date_updated: 2026-08-12T10:01:31Z day: '27' ddc: - '570' department: - _id: CaHe doi: 10.1242/dev.204261 external_id: isi: - '001525252300001' pmid: - '40576478' file: - access_level: open_access checksum: 808d8aa28df79d23fb661838d1fdc1be content_type: application/pdf creator: dernst date_created: 2025-07-23T08:43:01Z date_updated: 2025-07-23T08:43:01Z file_id: '20070' file_name: 2025_Development_Moriyama.pdf file_size: 25935563 relation: main_file success: 1 file_date_updated: 2025-07-23T08:43:01Z has_accepted_license: '1' intvolume: ' 152' isi: 1 issue: '12' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 152 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21343' abstract: - lang: eng 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: 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.' acknowledgement: While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278). article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Yik Tung full_name: Chan, Yik Tung id: c4c0afc8-9262-11ed-9231-d8b0bc743af1 last_name: Chan orcid: 0000-0001-8467-4106 citation: ama: Browning TD, Chan S. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 2025;12:1677-1691. doi:10.5802/jep.320 apa: Browning, T. D., & Chan, S. (2025). Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.320 chicago: Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2025. https://doi.org/10.5802/jep.320. ieee: T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” Journal de l’Ecole Polytechnique - Mathematiques, 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. mla: Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:10.5802/jep.320. short: T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691. corr_author: '1' das_tickbox: '0' date_created: 2026-02-22T23:01:36Z date_published: 2025-10-21T00:00:00Z date_updated: 2026-08-12T11:17:50Z day: '21' ddc: - '510' department: - _id: TiBr doi: 10.5802/jep.320 external_id: arxiv: - '2411.09264' file: - access_level: open_access checksum: 828577ea48ac6109d3e9dd1aeddd45c4 content_type: application/pdf creator: dernst date_created: 2026-02-24T07:56:34Z date_updated: 2026-02-24T07:56:34Z file_id: '21356' file_name: 2025_JEP_Browning.pdf file_size: 1003689 relation: main_file success: 1 file_date_updated: 2026-02-24T07:56:34Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1677-1691 project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication: Journal de l'Ecole Polytechnique - Mathematiques publication_identifier: eissn: - 2270-518X issn: - 2429-7100 publication_status: published publisher: Ecole Polytechnique quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Solubility of a resultant equation and applications tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20249' abstract: - lang: eng 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. 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_number: '81' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Florian Alexander full_name: Wilsch, Florian Alexander id: 560601DA-8D36-11E9-A136-7AC1E5697425 last_name: Wilsch orcid: 0000-0001-7302-8256 citation: ama: 'Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 2025;31(4). doi:10.1007/s00029-025-01074-1' apa: 'Browning, T. D., & Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. Springer Nature. https://doi.org/10.1007/s00029-025-01074-1' chicago: 'Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series. Springer Nature, 2025. https://doi.org/10.1007/s00029-025-01074-1.' ieee: 'T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” Selecta Mathematica New Series, vol. 31, no. 4. Springer Nature, 2025.' ista: 'Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.' mla: 'Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series, vol. 31, no. 4, 81, Springer Nature, 2025, doi:10.1007/s00029-025-01074-1.' short: T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025). corr_author: '1' das_tickbox: '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. date_created: 2025-08-31T22:01:31Z date_published: 2025-09-01T00:00:00Z date_updated: 2026-08-12T12:15:32Z day: '01' ddc: - '500' department: - _id: TiBr doi: 10.1007/s00029-025-01074-1 external_id: arxiv: - '2407.16315' isi: - '001552779800001' file: - access_level: open_access checksum: 89352f1f7e8d2b367ae5f4e9bf9eb1f5 content_type: application/pdf creator: dernst date_created: 2025-09-03T06:44:44Z date_updated: 2025-09-03T06:44:44Z file_id: '20281' file_name: 2025_SelectaMathematica_Browning.pdf file_size: 2484757 relation: main_file success: 1 file_date_updated: 2025-09-03T06:44:44Z has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '4' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 26AEDAB2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P32428 name: New frontiers of the Manin conjecture - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication: Selecta Mathematica New Series publication_identifier: eissn: - 1420-9020 issn: - 1022-1824 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/fwilsch/cubicpts record: - id: '22234' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: 'Integral points on cubic surfaces: heuristics and numerics' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20218' 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. 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_number: '333501' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Giorgio full_name: Volpe, Giorgio last_name: Volpe - first_name: Nuno A.M. full_name: Araújo, Nuno A.M. last_name: Araújo - first_name: Maria full_name: Guix, Maria last_name: Guix - first_name: Mark full_name: Miodownik, Mark last_name: Miodownik - first_name: Nicolas full_name: Martin, Nicolas last_name: Martin - first_name: Laura full_name: Alvarez, Laura last_name: Alvarez - first_name: Juliane full_name: Simmchen, Juliane last_name: Simmchen - first_name: Roberto Di full_name: Leonardo, Roberto Di last_name: Leonardo - first_name: Nicola full_name: Pellicciotta, Nicola last_name: Pellicciotta - first_name: Quentin full_name: Martinet, Quentin id: b37485a8-d343-11eb-a0e9-df8c484ef8ab last_name: Martinet orcid: 0000-0002-2916-6632 - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Wai Kit full_name: Ng, Wai Kit last_name: Ng - first_name: Dhruv full_name: Saxena, Dhruv last_name: Saxena - first_name: Riccardo full_name: Sapienza, Riccardo last_name: Sapienza - first_name: Sara full_name: Nadine, Sara last_name: Nadine - first_name: João F. full_name: Mano, João F. last_name: Mano - first_name: Reza full_name: Mahdavi, Reza last_name: Mahdavi - first_name: Caroline full_name: Beck Adiels, Caroline last_name: Beck Adiels - first_name: Joe full_name: Forth, Joe last_name: Forth - first_name: Christian full_name: Santangelo, Christian last_name: Santangelo - first_name: Stefano full_name: Palagi, Stefano last_name: Palagi - first_name: Ji Min full_name: Seok, Ji Min last_name: Seok - first_name: Victoria A. full_name: Webster-Wood, Victoria A. last_name: Webster-Wood - first_name: Shuhong full_name: Wang, Shuhong last_name: Wang - first_name: Lining full_name: Yao, Lining last_name: Yao - first_name: Amirreza full_name: Aghakhani, Amirreza last_name: Aghakhani - first_name: Thomas full_name: Barois, Thomas last_name: Barois - first_name: Hamid full_name: Kellay, Hamid last_name: Kellay - first_name: Corentin full_name: Coulais, Corentin last_name: Coulais - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke - first_name: Christopher J. full_name: Pierce, Christopher J. last_name: Pierce - first_name: Tianyu full_name: Wang, Tianyu last_name: Wang - first_name: Baxi full_name: Chong, Baxi last_name: Chong - first_name: Daniel I. full_name: Goldman, Daniel I. last_name: Goldman - first_name: Andreagiovanni full_name: Reina, Andreagiovanni last_name: Reina - first_name: Vito full_name: Trianni, Vito last_name: Trianni - first_name: Giovanni full_name: Volpe, Giovanni last_name: Volpe - first_name: Richard full_name: Beckett, Richard last_name: Beckett - first_name: Sean P. full_name: Nair, Sean P. last_name: Nair - first_name: Rachel full_name: Armstrong, Rachel last_name: Armstrong citation: ama: 'Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. Journal of Physics: Condensed Matter. 2025;37(33). doi:10.1088/1361-648X/adebd3' apa: 'Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/adebd3' chicago: 'Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” Journal of Physics: Condensed Matter. IOP Publishing, 2025. https://doi.org/10.1088/1361-648X/adebd3.' ieee: 'G. Volpe et al., “Roadmap for animate matter,” Journal of Physics: Condensed Matter, vol. 37, no. 33. IOP Publishing, 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.' mla: 'Volpe, Giorgio, et al. “Roadmap for Animate Matter.” Journal of Physics: Condensed Matter, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:10.1088/1361-648X/adebd3.' 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).' date_created: 2025-08-24T22:01:30Z date_published: 2025-08-18T00:00:00Z date_updated: 2026-08-12T14:00:12Z day: '18' ddc: - '530' department: - _id: JePa doi: 10.1088/1361-648X/adebd3 external_id: arxiv: - '2407.10623' isi: - '001550090200001' file: - access_level: open_access checksum: 7309274f78bed785b158bd290337f456 content_type: application/pdf creator: dernst date_created: 2025-09-02T07:22:48Z date_updated: 2025-09-02T07:22:48Z file_id: '20271' file_name: 2025_CondensedMatter_Volpe.pdf file_size: 8997829 relation: main_file success: 1 file_date_updated: 2025-09-02T07:22:48Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '33' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: 'Journal of Physics: Condensed Matter' publication_identifier: eissn: - 1361-648X issn: - 0953-8984 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Roadmap for animate matter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20453' abstract: - lang: eng 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.' 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. article_number: '405801' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Hamza full_name: Farooq, Hamza last_name: Farooq - first_name: Muhammad full_name: Nauman, Muhammad id: 32c21954-2022-11eb-9d5f-af9f93c24e71 last_name: Nauman orcid: 0000-0002-2111-4846 citation: ama: 'Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. 2025;37(40). doi:10.1088/1361-648X/ae0913' apa: 'Farooq, H., & Nauman, M. (2025). Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/ae0913' chicago: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” Journal of Physics: Condensed Matter. IOP Publishing, 2025. https://doi.org/10.1088/1361-648X/ae0913.' ieee: 'H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,” Journal of Physics: Condensed Matter, 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.' mla: 'Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” Journal of Physics: Condensed Matter, vol. 37, no. 40, 405801, IOP Publishing, 2025, doi:10.1088/1361-648X/ae0913.' short: 'H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).' corr_author: '1' date_created: 2025-10-12T22:01:26Z date_published: 2025-10-06T00:00:00Z date_updated: 2026-08-12T14:00:34Z day: '06' ddc: - '530' department: - _id: KiMo doi: 10.1088/1361-648X/ae0913 external_id: isi: - '001585824100001' pmid: - '40967257' file: - access_level: open_access checksum: b182856a5a655496e149afa49ec464f3 content_type: application/pdf creator: dernst date_created: 2025-10-13T06:34:15Z date_updated: 2025-10-13T06:34:15Z file_id: '20458' file_name: 2025_JourPhysicsCondMatter_Farooq.pdf file_size: 1709516 relation: main_file success: 1 file_date_updated: 2025-10-13T06:34:15Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '40' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: 'Journal of Physics: Condensed Matter' publication_identifier: eissn: - 1361-648X issn: - 0953-8984 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Non-linear magnetotropic susceptibility in FePS3 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2025' ... --- OA_type: closed access _id: '20219' abstract: - lang: eng 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. 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_number: '20250202' article_processing_charge: No article_type: original author: - first_name: Oran full_name: Ayalon, Oran last_name: Ayalon - first_name: Harikrishnan full_name: Rajendran, Harikrishnan id: 876b6b34-8ff4-11ec-97c9-8d95a7aae416 last_name: Rajendran citation: ama: Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 2025;22(229). doi:10.1098/rsif.2025.0202 apa: Ayalon, O., & Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. Royal Society. https://doi.org/10.1098/rsif.2025.0202 chicago: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface. Royal Society, 2025. https://doi.org/10.1098/rsif.2025.0202. ieee: O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” Journal of the Royal Society Interface, vol. 22, no. 229. Royal Society, 2025. ista: Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202. mla: Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface, vol. 22, no. 229, 20250202, Royal Society, 2025, doi:10.1098/rsif.2025.0202. short: O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025). corr_author: '1' date_created: 2025-08-24T22:01:30Z date_published: 2025-08-13T00:00:00Z date_updated: 2026-08-12T14:09:20Z day: '13' department: - _id: SyCr doi: 10.1098/rsif.2025.0202 external_id: isi: - '001548084900001' pmid: - '40799050' intvolume: ' 22' isi: 1 issue: '229' language: - iso: eng month: '08' oa_version: None pmid: 1 publication: Journal of the Royal Society Interface publication_identifier: eissn: - 1742-5662 issn: - 1742-5689 publication_status: published publisher: Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Interplay of asexual and sexual reproduction in bifunctional insects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2025' ... --- OA_place: repository OA_type: green _id: '19762' abstract: - lang: eng text: The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process. acknowledgement: "We thank A. Iñigo for assistance with imaging, and members of the Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency (AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1) to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship (JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012) to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council (101118729) to V.B., who also acknowledges financial support from AEI through the “Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S)." article_processing_charge: No author: - first_name: Adrián full_name: Cárdenas, Adrián last_name: Cárdenas - first_name: Irem full_name: Çelik, Irem last_name: Çelik - first_name: Alexandre full_name: Espinós, Alexandre last_name: Espinós - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Lara full_name: López-González, Lara last_name: López-González - first_name: Lucia full_name: del-Valle-Anton, Lucia last_name: del-Valle-Anton - first_name: Virginia full_name: Fernández, Virginia last_name: Fernández - first_name: Salma full_name: Amin, Salma last_name: Amin - first_name: Enrico full_name: Negri, Enrico last_name: Negri - first_name: Eduardo Fernández full_name: Ortuño, Eduardo Fernández last_name: Ortuño - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Víctor full_name: Borrell, Víctor last_name: Borrell biorxivid: 1 citation: ama: Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv. doi:10.1101/2025.05.22.655488 apa: Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton, L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv. https://doi.org/10.1101/2025.05.22.655488 chicago: Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.22.655488. ieee: A. Cárdenas et al., “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” bioRxiv. . ista: Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv, 10.1101/2025.05.22.655488. mla: Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” BioRxiv, doi:10.1101/2025.05.22.655488. short: A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton, V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv (n.d.). date_created: 2025-05-29T10:45:55Z date_published: 2025-05-23T00:00:00Z date_updated: 2026-08-13T07:18:38Z day: '23' department: - _id: SiHi doi: 10.1101/2025.05.22.655488 external_id: biorxivid: - 10.1101/2025.05.22.655488 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.22.655488 month: '05' oa: 1 oa_version: Preprint project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: bioRxiv publication_status: submitted status: public title: Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development tmp: 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '19717' abstract: - lang: eng text: Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise. acknowledgement: "We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n" article_processing_charge: No author: - first_name: I full_name: Varela-Martínez, I last_name: Varela-Martínez - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: J. full_name: Garcia-Marqués, J. last_name: Garcia-Marqués - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: M. full_name: Nieto, M. last_name: Nieto citation: ama: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv. doi:10.1101/2025.05.07.652665 apa: Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., & Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv. https://doi.org/10.1101/2025.05.07.652665 chicago: Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.07.652665. ieee: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” bioRxiv. . ista: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, 10.1101/2025.05.07.652665. mla: Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv, doi:10.1101/2025.05.07.652665. short: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.). date_created: 2025-05-20T10:19:29Z date_published: 2025-05-07T00:00:00Z date_updated: 2026-08-13T07:16:48Z day: '07' department: - _id: SiHi doi: 10.1101/2025.05.07.652665 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.07.652665 month: '05' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: submitted status: public title: Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '19674' abstract: - lang: eng text: 'When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets).' acknowledgement: "The authors gratefully acknowledge Volkan Cevher for an insightful discussion about sparse recovery algorithms, Alex Smola for valuable feedback on the experiments, and Marco Baroni for an engaging conversation on the phenomenon of head specialization in NLP.\r\n" article_number: '2411.00246' article_processing_charge: No arxiv: 1 author: - first_name: Lorenzo full_name: Basile, Lorenzo last_name: Basile - first_name: Valentino full_name: Maiorca, Valentino last_name: Maiorca - first_name: Luca full_name: Bortolussi, Luca last_name: Bortolussi - first_name: Emanuele full_name: Rodolà, Emanuele last_name: Rodolà - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv. doi:10.48550/arXiv.2411.00246 apa: Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., & Locatello, F. (n.d.). ResiDual transformer alignment with spectral decomposition. arXiv. https://doi.org/10.48550/arXiv.2411.00246 chicago: Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2411.00246. ieee: L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual transformer alignment with spectral decomposition,” arXiv. . ista: Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246. mla: Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.” ArXiv, 2411.00246, doi:10.48550/arXiv.2411.00246. short: L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.). date_created: 2025-05-11T22:02:41Z date_published: 2025-04-14T00:00:00Z date_updated: 2026-08-13T07:33:41Z day: '14' ddc: - '000' department: - _id: FrLo doi: 10.48550/arXiv.2411.00246 external_id: arxiv: - '2411.00246' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2411.00246 month: '04' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: ResiDual transformer alignment with spectral decomposition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20167' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön citation: ama: Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:10.15479/AT-ISTA-20167 apa: Schön, H. (2025). The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20167 chicago: Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20167. ieee: H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025. ista: Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. mla: Schön, Hanna. The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20167. short: H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-13T11:13:13Z date_published: 2025-08-13T00:00:00Z date_updated: 2026-08-13T13:05:37Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MaDe doi: 10.15479/AT-ISTA-20167 doi_confirm: '1' file: - access_level: closed checksum: b40c74404b8d9593802dabf57bfdf10f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hschoen date_created: 2025-09-08T14:33:50Z date_updated: 2025-09-09T08:57:04Z file_id: '20311' file_name: 2025_Schoen_Hanna_Thesis.docx file_size: 78812587 relation: source_file - access_level: closed checksum: 16abc3ff66396ce2457fe07ffa8bed90 content_type: application/pdf creator: hschoen date_created: 2025-09-11T14:20:59Z date_updated: 2026-08-13T13:05:36Z embargo: 2027-03-15 embargo_to: open_access file_id: '20347' file_name: 2025_Schoen_Hanna_Thesis.pdf file_size: 9667057 relation: main_file file_date_updated: 2026-08-13T13:05:36Z has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '171' project: - _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E grant_number: 209504/A/17/Z name: Molecular mechanisms of neural circuit function - _id: 23813290-32DE-11EA-91FC-C7463DDC885E grant_number: ALTF 302-2019 name: Control of gene expression at the endoplasmic reticulum publication_identifier: isbn: - 978-3-99078-061-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 title: The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20538' abstract: - lang: eng text: In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70. article_number: '169465' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sonja full_name: Knödlstorfer, Sonja last_name: Knödlstorfer - first_name: Giorgia full_name: Toscano, Giorgia id: 334a5e40-8747-11f0-b671-ba1f5154b4b4 last_name: Toscano - first_name: Aleksandra L. full_name: Ptaszek, Aleksandra L. last_name: Ptaszek - first_name: Georg full_name: Kontaxis, Georg last_name: Kontaxis - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Jakob full_name: Schneider, Jakob id: 64368429-eb97-11eb-a6c2-c980b1f44415 last_name: Schneider - first_name: Katharina full_name: Maier, Katharina last_name: Maier - first_name: Anna full_name: Kapitonova, Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - first_name: Roman J. full_name: Lichtenecker, Roman J. last_name: Lichtenecker - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Robert full_name: Konrat, Robert last_name: Konrat citation: ama: Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169465 apa: Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169465 chicago: Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology. Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169465. ieee: S. Knödlstorfer et al., “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025. ista: Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465. mla: Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology, vol. 437, no. 23, 169465, Elsevier, 2025, doi:10.1016/j.jmb.2025.169465. short: S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025). date_created: 2025-10-26T23:01:35Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-08-13T14:19:02Z day: '01' ddc: - '540' department: - _id: PaSc - _id: GradSch doi: 10.1016/j.jmb.2025.169465 external_id: pmid: - '41016549' file: - access_level: open_access checksum: feb92f9c79032c261165f4ca573f444a content_type: application/pdf creator: dernst date_created: 2025-12-30T10:29:08Z date_updated: 2025-12-30T10:29:08Z file_id: '20915' file_name: 2025_JourMolecularBiology_Knoedlstorfer.pdf file_size: 3076611 relation: main_file success: 1 file_date_updated: 2025-12-30T10:29:08Z has_accepted_license: '1' intvolume: ' 437' issue: '23' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0 grant_number: I06223 name: Structure and mechanism of the mitochondrial MIM insertase - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Journal of Molecular Biology publication_identifier: eissn: - 1089-8638 issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 437 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20258' abstract: - lang: eng text: The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: This work was supported financially by the Austrian Science Fund (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent support of the NMR facility. article_number: '169379' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Darja full_name: Rohden, Darja id: 81dc668a-19fa-11f0-bf31-d56534059ef3 last_name: Rohden - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Anna full_name: Kapitonova, Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - first_name: Benjamin full_name: Tatman, Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - first_name: Roman J. full_name: Lichtenecker, Roman J. last_name: Lichtenecker - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169379 apa: Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., & Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169379 chicago: Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology. Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169379. ieee: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P. Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025. ista: Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 437(23), 169379. mla: Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology, vol. 437, no. 23, 169379, Elsevier, 2025, doi:10.1016/j.jmb.2025.169379. short: D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda, Journal of Molecular Biology 437 (2025). corr_author: '1' date_created: 2025-08-31T22:01:33Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-08-13T14:19:01Z day: '01' ddc: - '540' department: - _id: PaSc doi: 10.1016/j.jmb.2025.169379 external_id: isi: - '001618289100020' file: - access_level: open_access checksum: 90d50594d8ea9860ac5da41297992847 content_type: application/pdf creator: dernst date_created: 2025-12-29T14:51:40Z date_updated: 2025-12-29T14:51:40Z file_id: '20876' file_name: 2025_JourMolecularBiology_Rohden.pdf file_size: 2270555 relation: main_file success: 1 file_date_updated: 2025-12-29T14:51:40Z has_accepted_license: '1' intvolume: ' 437' isi: 1 issue: '23' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Journal of Molecular Biology publication_identifier: eissn: - 1089-8638 issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19956' relation: research_data status: public scopus_import: '1' status: public title: Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 437 year: '2025' ... --- _id: '19956' abstract: - lang: eng text: The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR acknowledged_ssus: - _id: NMR - _id: LifeSc article_processing_charge: No author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schanda P. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. 2025. doi:10.15479/AT-ISTA-19956 apa: Schanda, P. (2025). Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19956 chicago: Schanda, Paul. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19956. ieee: P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025. ista: Schanda P. 2025. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme, Institute of Science and Technology Austria, 10.15479/AT-ISTA-19956. mla: Schanda, Paul. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19956. short: P. Schanda, (2025). contributor: - contributor_type: researcher first_name: Darja last_name: Rohden - contributor_type: researcher first_name: Federico last_name: Napoli - contributor_type: researcher first_name: Ben last_name: Tatman - contributor_type: researcher first_name: Paul last_name: Schanda corr_author: '1' date_created: 2025-07-03T04:21:37Z date_published: 2025-07-03T00:00:00Z date_updated: 2026-08-13T14:19:01Z day: '03' ddc: - '572' department: - _id: PaSc doi: 10.15479/AT-ISTA-19956 file: - access_level: open_access checksum: a2ef61aa9fb5313c7d426913eb0482c0 content_type: application/octet-stream creator: pschanda date_created: 2025-07-03T10:30:14Z date_updated: 2025-07-03T10:30:14Z file_id: '19960' file_name: README file_size: 1160 relation: main_file success: 1 - access_level: open_access checksum: 8fb77b96d0fcc95c9903005652207a8c content_type: application/zip creator: pschanda date_created: 2025-07-03T10:30:55Z date_updated: 2025-07-03T10:30:55Z file_id: '19961' file_name: data_Arg_MASNMR_Rohden.zip file_size: 128597184 relation: main_file success: 1 - access_level: open_access checksum: a60cc16d20b089c4bef94040a99cfba5 content_type: application/x-xz creator: pschanda date_created: 2025-08-14T07:06:58Z date_updated: 2025-08-14T07:06:58Z file_id: '20172' file_name: 20240903_ubi_DN_Argd1C13_2D_spectra.tar.xz file_size: 4766564 relation: main_file success: 1 file_date_updated: 2025-08-14T07:06:58Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publisher: Institute of Science and Technology Austria related_material: record: - id: '20258' relation: used_in_publication status: public status: public title: Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- OA_place: publisher _id: '19395' abstract: - lang: eng text: "Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood." acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer citation: ama: 'Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant development. 2025. doi:10.15479/AT-ISTA-19395' apa: 'Monzer, A. (2025). Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395' chicago: 'Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.' ieee: 'A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.' ista: 'Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.' mla: 'Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395.' short: 'A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-03-12T14:25:42Z date_published: 2025-03-13T00:00:00Z date_updated: 2026-08-14T09:33:46Z day: '13' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19395 doi_confirm: '1' file: - access_level: open_access checksum: 9a3dd03bb4ec6b9907a325c3c4e8a1d7 content_type: application/pdf creator: amonzer date_created: 2025-03-12T14:14:49Z date_updated: 2025-03-12T14:14:49Z file_id: '19396' file_name: Final Thesis Aline Monzer.pdf file_size: 13119670 relation: main_file success: 1 - access_level: closed checksum: a353ce1ee2eabce37bca35499e76dbf1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amonzer date_created: 2025-03-12T14:15:19Z date_updated: 2025-04-01T07:55:27Z file_id: '19397' file_name: Thesis Aline.docx file_size: 13774837 relation: source_file file_date_updated: 2025-04-01T07:55:27Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: eisbn: - 978-3-99078-054-1 eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '14826' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public - id: '19398' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Cell-surface auxin signaling: Linking molecular pathways to plant development' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ...