[{"ec_funded":1,"oa_version":"Published Version","day":"21","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}],"year":"2023","date_published":"2023-11-21T00:00:00Z","citation":{"ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587"},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:14587","degree_awarded":"PhD","publication_status":"published","date_updated":"2026-04-07T13:28:13Z","month":"11","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","date_created":"2023-11-21T11:41:05Z","status":"public","supervisor":[{"orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["515"],"file":[{"file_size":2881100,"relation":"main_file","success":1,"access_level":"open_access","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","date_created":"2023-11-29T09:09:31Z","creator":"amarvegg","file_id":"14626","content_type":"application/pdf","date_updated":"2023-11-29T09:09:31Z","file_name":"thesis_Marveggio.pdf"},{"content_type":"application/zip","file_name":"Thesis_Marveggio.zip","date_updated":"2024-03-20T12:28:32Z","creator":"amarvegg","file_id":"14627","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","date_created":"2023-11-29T09:10:19Z","relation":"source_file","file_size":10189696,"access_level":"closed"}],"page":"228","oa":1,"related_material":{"record":[{"status":"public","id":"11842","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14597","status":"public"}]},"_id":"14587","OA_place":"publisher","corr_author":"1","file_date_updated":"2024-03-20T12:28:32Z","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","author":[{"first_name":"Alice","full_name":"Marveggio, Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation"},{"abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"day":"12","oa_version":"Published Version","ec_funded":1,"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T13:28:30Z","month":"12","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","date_published":"2023-12-12T00:00:00Z","year":"2023","citation":{"ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651"},"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:14651","file":[{"access_level":"open_access","success":1,"relation":"main_file","file_size":34101468,"date_created":"2023-12-13T15:37:55Z","checksum":"520bdb61e95e66070e02824947d2c5fa","file_id":"14684","creator":"larathoo","file_name":"Phd_Thesis_LA.pdf","date_updated":"2023-12-13T15:37:55Z","content_type":"application/pdf"},{"content_type":"application/zip","file_name":"Phd_Thesis_LA.zip","date_updated":"2023-12-14T08:58:18Z","file_id":"14685","creator":"larathoo","checksum":"d8e59afd0817c98fba2564a264508e5c","date_created":"2023-12-13T15:42:23Z","relation":"source_file","file_size":31052872,"access_level":"closed"},{"file_name":"Supplementary_Materials.zip","date_updated":"2023-12-14T08:58:18Z","content_type":"application/zip","creator":"larathoo","file_id":"14681","date_created":"2023-12-11T19:24:59Z","checksum":"9a778c949932286f4519e1f1fca2820d","access_level":"closed","relation":"supplementary_material","file_size":10713896}],"ddc":["570"],"page":"96","supervisor":[{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"date_created":"2023-12-11T19:30:37Z","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"file_date_updated":"2023-12-14T08:58:18Z","corr_author":"1","author":[{"last_name":"Arathoon","full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","id":"11411","status":"public"}]},"oa":1,"_id":"14651","OA_place":"publisher"},{"ddc":["530"],"file":[{"access_level":"closed","relation":"main_file","file_size":63734746,"date_created":"2023-03-23T12:49:23Z","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_id":"12745","creator":"cchlebak","file_name":"Thesis_Riedl_2023.pdf","date_updated":"2023-11-24T11:57:46Z","content_type":"application/pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files."},{"checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","date_created":"2023-03-23T12:54:34Z","file_size":339473651,"relation":"source_file","access_level":"closed","content_type":"application/octet-stream","file_name":"Thesis_Riedl_2023_source.rar","date_updated":"2023-09-24T22:30:03Z","creator":"cchlebak","file_id":"12746","embargo_to":"open_access"}],"page":"260","date_created":"2023-03-15T13:22:13Z","status":"public","supervisor":[{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"corr_author":"1","file_date_updated":"2023-11-24T11:57:46Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","first_name":"Michael"}],"type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"461"},{"status":"public","id":"10791","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"relation":"part_of_dissertation","id":"10703","status":"public"},{"id":"14530","status":"public","relation":"new_edition"}]},"_id":"12726","OA_place":"publisher","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"oa_version":"None","day":"23","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-07T13:29:13Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"month":"03","title":"Synchronization in collectively moving active matter","date_published":"2023-03-23T00:00:00Z","year":"2023","citation":{"short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12726","publication_status":"published","degree_awarded":"PhD"},{"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0003-4844-6311","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","last_name":"Riedl"}],"file_date_updated":"2023-11-15T09:52:54Z","corr_author":"1","OA_place":"publisher","_id":"14530","related_material":{"record":[{"id":"461","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10791","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"id":"10703","status":"public","relation":"part_of_dissertation"},{"relation":"old_edition","status":"public","id":"12726"}]},"oa":1,"page":"260","file":[{"date_created":"2023-11-15T09:52:54Z","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","success":1,"access_level":"open_access","relation":"main_file","file_size":36743942,"file_name":"Thesis_Riedl_2023_corr.pdf","date_updated":"2023-11-15T09:52:54Z","content_type":"application/pdf","creator":"mriedl","file_id":"14536"}],"ddc":["530","570"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"status":"public","date_created":"2023-11-15T09:59:03Z","title":"Synchronization in collectively moving active matter","month":"11","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"date_updated":"2026-04-07T13:29:13Z","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/14530","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023."},"year":"2023","date_published":"2023-11-16T00:00:00Z","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"day":"16","oa_version":"Updated Version"},{"supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","first_name":"Uli"}],"status":"public","date_created":"2023-07-31T10:20:55Z","has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"creator":"skoese","file_id":"13333","content_type":"application/x-zip-compressed","file_name":"Exterior Algebra and Combinatorics.zip","date_updated":"2023-07-31T10:16:32Z","file_size":28684,"relation":"source_file","access_level":"closed","checksum":"96ee518d796d02af71395622c45de03c","date_created":"2023-07-31T10:16:32Z"},{"checksum":"f610f4713f88bc477de576aaa46b114e","date_created":"2023-08-03T15:28:55Z","relation":"main_file","file_size":4953418,"access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"thesis-pdfa.pdf","date_updated":"2023-08-03T15:28:55Z","file_id":"13480","creator":"skoese"}],"ddc":["510","516"],"page":"26","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"12680","status":"public"}]},"OA_place":"publisher","_id":"13331","file_date_updated":"2023-08-03T15:28:55Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Seyda","orcid":"0009-0008-0457-9730","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","last_name":"Köse"}],"day":"31","oa_version":"Published Version","alternative_title":["ISTA Master's Thesis"],"abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"citation":{"mla":"Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331","apa":"Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023."},"date_published":"2023-07-31T00:00:00Z","year":"2023","publication_status":"published","degree_awarded":"MS","doi":"10.15479/at:ista:13331","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2791-4585"]},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"month":"07","date_updated":"2026-04-07T13:29:29Z","title":"Exterior algebra and combinatorics"},{"isi":1,"article_number":"113363","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","date_updated":"2026-04-07T13:29:28Z","month":"06","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"publication_identifier":{"issn":["0012-365X"]},"article_processing_charge":"No","publisher":"Elsevier","doi":"10.1016/j.disc.2023.113363","publication_status":"published","date_published":"2023-06-01T00:00:00Z","year":"2023","citation":{"ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","mla":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” Discrete Mathematics, vol. 346, no. 6, 113363, Elsevier, 2023, doi:10.1016/j.disc.2023.113363.","ieee":"G. Ivanov and S. Köse, “Erdős-Ko-Rado and Hilton-Milner theorems for two-forms,” Discrete Mathematics, vol. 346, no. 6. Elsevier, 2023.","apa":"Ivanov, G., & Köse, S. (2023). Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2023.113363","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","chicago":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” Discrete Mathematics. Elsevier, 2023. https://doi.org/10.1016/j.disc.2023.113363.","ama":"Ivanov G, Köse S. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 2023;346(6). doi:10.1016/j.disc.2023.113363"},"article_type":"letter_note","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2201.10892"}],"abstract":[{"lang":"eng","text":"The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines."}],"external_id":{"arxiv":["2201.10892"],"isi":["001189844500001"]},"quality_controlled":"1","volume":346,"day":"01","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","orcid":"0000-0002-5021-3982","first_name":"Grigory"},{"first_name":"Seyda","orcid":"0009-0008-0457-9730","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","full_name":"Köse, Seyda"}],"type":"journal_article","corr_author":"1","issue":"6","arxiv":1,"_id":"12680","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13331"}]},"intvolume":" 346","publication":"Discrete Mathematics","language":[{"iso":"eng"}],"date_created":"2023-02-26T23:01:00Z","scopus_import":"1","status":"public"},{"doi":"10.15479/at:ista:13074","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","citation":{"ieee":"A. Krumes, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","mla":"Krumes, Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","ista":"Krumes A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","ama":"Krumes A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","chicago":"Krumes, Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","short":"A. Krumes, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","apa":"Krumes, A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074"},"date_published":"2023-05-23T00:00:00Z","year":"2023","title":"Efficiency and generalization of sparse neural networks","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"month":"05","date_updated":"2026-04-07T13:30:20Z","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Published Version","day":"23","abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"OA_place":"publisher","_id":"13074","related_material":{"record":[{"status":"public","id":"13053","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11458"},{"status":"public","id":"12299","relation":"part_of_dissertation"}]},"oa":1,"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Elena-Alexandra","last_name":"Peste","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","file_date_updated":"2023-05-24T16:12:59Z","language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2023-05-23T17:07:53Z","status":"public","supervisor":[{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"page":"147","ddc":["000"],"file":[{"date_created":"2023-05-24T16:11:16Z","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"access_level":"open_access","relation":"main_file","file_size":2152072,"file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","date_updated":"2023-05-24T16:11:16Z","content_type":"application/pdf","file_id":"13087","creator":"epeste"},{"creator":"epeste","file_id":"13088","file_name":"PhD_Thesis_APeste.zip","date_updated":"2023-05-24T16:12:59Z","content_type":"application/zip","access_level":"closed","relation":"source_file","file_size":1658293,"date_created":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60"}]},{"oa_version":"Published Version","day":"01","ec_funded":1,"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2207.14200"]},"quality_controlled":"1","main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"conference":{"location":"Kigali, Rwanda ","start_date":"2023-05-01","name":"ICLR: International Conference on Learning Representations","end_date":"2023-05-05"},"citation":{"apa":"Krumes, A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (2023). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda : OpenReview.","short":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , OpenReview, 2023.","chicago":"Krumes, Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations . OpenReview, 2023.","ama":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations . OpenReview; 2023.","ista":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. 2023. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","mla":"Krumes, Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations , OpenReview, 2023.","ieee":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda , 2023."},"year":"2023","date_published":"2023-05-01T00:00:00Z","publication_status":"published","publisher":"OpenReview","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"month":"05","date_updated":"2026-04-07T13:30:19Z","title":"CrAM: A Compression-Aware Minimizer","date_created":"2023-05-23T11:36:18Z","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"publication":"11th International Conference on Learning Representations ","file":[{"creator":"dernst","file_id":"17294","file_name":"2023_ICLR_Peste.pdf","date_updated":"2024-07-22T09:09:45Z","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_size":458201,"date_created":"2024-07-22T09:09:45Z","checksum":"a6eec897e13a91cdc3eeaf309801752c"}],"ddc":["000"],"oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/CrAM"}],"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"_id":"13053","arxiv":1,"file_date_updated":"2024-07-22T09:09:45Z","corr_author":"1","type":"conference","author":[{"first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","last_name":"Peste"},{"last_name":"Vladu","full_name":"Vladu, Adrian","first_name":"Adrian"},{"last_name":"Kurtic","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","full_name":"Kurtic, Eldar","first_name":"Eldar"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)."},{"abstract":[{"lang":"eng","text":"Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments."}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","day":"30","ec_funded":1,"title":"Adaptive mutation in E. coli modulated by luxS","date_updated":"2026-04-07T13:29:59Z","month":"11","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:14641","year":"2023","date_published":"2023-11-30T00:00:00Z","citation":{"short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641."},"page":"104","file":[{"embargo_to":"open_access","creator":"mhenness","file_id":"14648","content_type":"application/vnd.oasis.opendocument.text","file_name":"mike_thesis_v06-12-2023.odt","date_updated":"2024-11-30T23:30:05Z","relation":"source_file","file_size":46405919,"access_level":"closed","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_created":"2023-12-06T13:13:26Z"},{"date_created":"2023-12-06T13:14:15Z","checksum":"f5203a61eddaf35235bbc51904d73982","access_level":"closed","relation":"main_file","file_size":21282155,"date_updated":"2025-07-17T11:20:25Z","file_name":"mike_thesis_v06-12-2023.pdf","embargo":"2026-07-18","content_type":"application/pdf","embargo_to":"open_access","creator":"mhenness","file_id":"14649"},{"checksum":"902102d26d30e74dbd6cdd70a65820c3","date_created":"2025-05-20T12:59:12Z","file_size":45847968,"relation":"other","access_level":"closed","content_type":"application/pdf","description":"for printing purposes only","date_updated":"2025-05-20T22:31:34Z","file_name":"2023_Hennessey_Michael_Thesis_print.pdf","title":"Print version","creator":"cchlebak","file_id":"19720","embargo_to":"open_access"}],"ddc":["570"],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"date_created":"2023-12-04T13:17:37Z","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"status":"public","author":[{"full_name":"Hennessey-Wesen, Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","last_name":"Hennessey-Wesen","first_name":"Mike"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","file_date_updated":"2025-07-17T11:20:25Z","corr_author":"1","_id":"14641","OA_place":"publisher"},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","day":"10","ec_funded":1,"abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"publication_status":"published","degree_awarded":"PhD","doi":"10.15479/14506","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","citation":{"chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria."},"date_published":"2023-11-10T00:00:00Z","year":"2023","title":"Advances in efficiency and privacy in payment channel network analysis","month":"11","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"date_updated":"2026-04-07T13:29:45Z","has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2023-11-10T08:10:43Z","status":"public","page":"162","file":[{"access_level":"closed","file_size":3037720,"relation":"source_file","date_created":"2023-11-23T10:29:55Z","checksum":"521c72818d720a52b377207b2ee87b6a","creator":"cchlebak","file_id":"14598","file_name":"thesis_yeo.zip","date_updated":"2023-11-23T10:29:55Z","content_type":"application/x-zip-compressed"},{"checksum":"0ed5d16899687aecf13d843c9878c9f2","date_created":"2023-11-23T10:30:08Z","file_size":2717256,"relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"thesis_yeo.pdf","date_updated":"2023-11-23T10:30:08Z","creator":"cchlebak","file_id":"14599"}],"ddc":["000"],"OA_place":"publisher","_id":"14506","related_material":{"record":[{"relation":"part_of_dissertation","status":"deleted","id":"13238"},{"id":"9969","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14490"}]},"oa":1,"type":"dissertation","author":[{"first_name":"Michelle X","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2023-11-23T10:30:08Z","corr_author":"1"},{"isi":1,"title":"Lightning creation games","department":[{"_id":"KrPi"}],"month":"10","date_updated":"2026-04-07T13:29:44Z","doi":"10.1109/ICDCS57875.2023.00037","publisher":"IEEE","publication_identifier":{"isbn":["9798350339864"],"eissn":["2575-8411"]},"article_processing_charge":"No","publication_status":"published","citation":{"short":"Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.","apa":"Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning creation games. In 43rd International Conference on Distributed Computing Systems (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037","ama":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: 43rd International Conference on Distributed Computing Systems. Vol 2023. IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037","chicago":"Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In 43rd International Conference on Distributed Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.","ista":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613.","ieee":"Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in 43rd International Conference on Distributed Computing Systems, Hong Kong, China, 2023, vol. 2023, pp. 603–613.","mla":"Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13, doi:10.1109/ICDCS57875.2023.00037."},"year":"2023","date_published":"2023-10-11T00:00:00Z","conference":{"start_date":"2023-07-18","location":"Hong Kong, China","name":"ICDCS: International Conference on Distributed Computing Systems","end_date":"2023-07-21"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.16006"}],"abstract":[{"text":"Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.","lang":"eng"}],"external_id":{"arxiv":["2306.16006"],"isi":["001081242600053"]},"quality_controlled":"1","oa_version":"Preprint","day":"11","volume":2023,"type":"conference","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666.","author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"first_name":"Tomasz","last_name":"Lizurej","full_name":"Lizurej, Tomasz"},{"full_name":"Michalak, Tomasz","last_name":"Michalak","first_name":"Tomasz"},{"first_name":"Michelle X","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"_id":"14490","oa":1,"related_material":{"record":[{"status":"public","id":"14506","relation":"dissertation_contains"}]},"page":"603-613","intvolume":" 2023","language":[{"iso":"eng"}],"publication":"43rd International Conference on Distributed Computing Systems","status":"public","date_created":"2023-11-05T23:00:54Z","scopus_import":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ali","last_name":"Mohammadi","full_name":"Mohammadi, Ali"},{"full_name":"Pham, Thang","last_name":"Pham","first_name":"Thang"},{"full_name":"Wang, Yiting","id":"1917d194-076e-11ed-97cd-837255f88785","last_name":"Wang","orcid":"0000-0002-2856-767X","first_name":"Yiting"}],"type":"journal_article","issue":"4","arxiv":1,"_id":"13128","oa":1,"page":"1280-1295","intvolume":" 66","publication":"Canadian Mathematical Bulletin","language":[{"iso":"eng"}],"date_created":"2023-06-11T22:00:40Z","scopus_import":"1","status":"public","isi":1,"title":"An energy decomposition theorem for matrices and related questions","date_updated":"2026-04-08T13:04:49Z","month":"12","department":[{"_id":"GradSch"}],"article_processing_charge":"No","publisher":"Cambridge University Press","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"doi":"10.4153/S000843952300036X","publication_status":"published","year":"2023","date_published":"2023-12-01T00:00:00Z","citation":{"ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” Canadian Mathematical Bulletin, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:10.4153/S000843952300036X.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 2023;66(4):1280-1295. doi:10.4153/S000843952300036X","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin. Cambridge University Press, 2023. https://doi.org/10.4153/S000843952300036X.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","apa":"Mohammadi, A., Pham, T., & Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. Cambridge University Press. https://doi.org/10.4153/S000843952300036X"},"article_type":"original","abstract":[{"lang":"eng","text":"Given 𝐴 ⊆𝐺𝐿2(𝔽𝑞), we prove that there exist disjoint subsets 𝐵,𝐶 ⊆𝐴 such that 𝐴 =𝐵 ⊔𝐶 and their additive and multiplicative energies satisfying\r\nmax{𝐸+(𝐵),𝐸×(𝐶)}≪|𝐴|3/𝑀(|𝐴|), where\r\n𝑀(|𝐴|)=min{𝑞4/3/|𝐴|1/3(log|𝐴|)2/3, |𝐴|4/5/𝑞13/5(log|𝐴|)27/10}.\r\n \r\nWe also study some related questions on moderate expanders over matrix rings, namely, for 𝐴,𝐵,𝐶 ⊆𝐺𝐿2(𝔽𝑞), we have\r\n|𝐴𝐵+𝐶|, |(𝐴+𝐵)𝐶|≫𝑞4,\r\n whenever |𝐴||𝐵||𝐶| ≫𝑞10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, 𝐹𝑜𝑟𝑢𝑚𝑀𝑎𝑡ℎ., 31, 951–970)."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"quality_controlled":"1","external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"day":"01","oa_version":"Preprint","volume":66},{"status":"public","date_created":"2023-02-26T12:24:21Z","scopus_import":"1","keyword":["General Neuroscience"],"has_accepted_license":"1","publication":"Current Opinion in Neurobiology","language":[{"iso":"eng"}],"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":1787894,"date_created":"2023-08-16T12:29:06Z","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","creator":"dernst","file_id":"14071","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","date_updated":"2023-08-16T12:29:06Z","content_type":"application/pdf"}],"ddc":["570"],"pmid":1,"intvolume":" 79","oa":1,"_id":"12679","file_date_updated":"2023-08-16T12:29:06Z","corr_author":"1","issue":"4","acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","author":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Published Version","day":"01","volume":79,"ec_funded":1,"external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"quality_controlled":"1","project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression."}],"article_type":"review","year":"2023","date_published":"2023-04-01T00:00:00Z","citation":{"apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023."},"publication_status":"published","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0959-4388"]},"doi":"10.1016/j.conb.2023.102695","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-15T08:23:06Z","department":[{"_id":"SiHi"}],"month":"04","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral 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Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","file_date_updated":"2023-08-04T13:19:47Z","corr_author":"1","_id":"13126","related_material":{"link":[{"description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ","url":"https://pub.ista.ac.at/group_danzl/data/CATS/","relation":"research_data"}],"record":[{"relation":"used_in_publication","status":"public","id":"14257"}]},"oa":1,"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"project":[{"grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"},{"grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635"}],"oa_version":"Published Version","day":"04","ec_funded":1,"title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"month":"08","contributor":[{"first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431"},{"id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Stefanickova","first_name":"Hana"},{"orcid":"0000-0002-8698-3823","first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207"},{"orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino"},{"first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","last_name":"Czech"},{"last_name":"Höftberger","first_name":"Romana"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"date_updated":"2026-04-14T08:34:35Z","doi":"10.15479/AT:ISTA:13126","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"short":"J.G. Danzl, (2023).","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126.","ieee":"J. G. 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Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265."},"OA_type":"hybrid","abstract":[{"text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. 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Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. 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Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817.","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817.","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817","apa":"Danzl, J. G. (2023). 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It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"oa_version":"Published Version","day":"19","type":"research_data","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. 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LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"article_type":"letter_note","oa_version":"None","day":"01","volume":20,"quality_controlled":"1","external_id":{"isi":["001025621500002"]},"corr_author":"1","issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Velicky","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431"}],"type":"journal_article","related_material":{"record":[{"relation":"extended_version","status":"public","id":"13267"}]},"_id":"14770","intvolume":" 20","page":"1141-1142","scopus_import":"1","date_created":"2024-01-10T08:07:15Z","status":"public","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"publication":"Nature Methods","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans."}],"project":[{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","day":"31","ec_funded":1,"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","date_updated":"2026-04-14T08:34:36Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"month":"05","degree_awarded":"PhD","publication_status":"published","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:13107","date_published":"2023-05-31T00:00:00Z","year":"2023","citation":{"chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.","ama":"Knaus L. 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Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"},{"first_name":"Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"full_name":"Malzl, Daniel","last_name":"Malzl","first_name":"Daniel"},{"full_name":"Gerykova Bujalkova, Maria","last_name":"Gerykova Bujalkova","first_name":"Maria"},{"first_name":"Mateja","last_name":"Smogavec","full_name":"Smogavec, Mateja"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A.","first_name":"Lena A."},{"first_name":"Sarah","full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","last_name":"Gorkiewicz"},{"orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","last_name":"Amberg"},{"first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Knittl-Frank","full_name":"Knittl-Frank, Christian"},{"last_name":"Tassinari","full_name":"Tassinari, Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","first_name":"Marianna"},{"first_name":"Nuno","full_name":"Maulide, Nuno","last_name":"Maulide"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"ec_funded":1,"oa_version":"Published Version","day":"27","volume":186,"project":[{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000991468700001"],"pmid":["36996814"]},"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"citation":{"short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037","chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier, 2023. https://doi.org/10.1016/j.cell.2023.02.037.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","ieee":"L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:10.1016/j.cell.2023.02.037."},"date_published":"2023-04-27T00:00:00Z","year":"2023","doi":"10.1016/j.cell.2023.02.037","publisher":"Elsevier","publication_identifier":{"issn":["0092-8674"]},"article_processing_charge":"Yes (via OA deal)","publication_status":"published","month":"04","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"date_updated":"2026-04-14T08:34:36Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival"},{"abstract":[{"text":"Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling.","lang":"eng"}],"article_type":"review","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"}],"quality_controlled":"1","external_id":{"isi":["001082823000006"],"pmid":["37418774"]},"day":"16","oa_version":"Published Version","volume":39,"ec_funded":1,"title":"Control of tissue development by morphogens","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"AnKi"}],"month":"10","date_updated":"2025-12-30T10:57:08Z","publication_status":"published","doi":"10.1146/annurev-cellbio-020823-011522","publication_identifier":{"eissn":["1530-8995"],"issn":["1081-0706"]},"article_processing_charge":"Yes (in subscription journal)","publisher":"Annual Reviews","citation":{"apa":"Kicheva, A., & Briscoe, J. (2023). Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-020823-011522","short":"A. Kicheva, J. Briscoe, Annual Review of Cell and Developmental Biology 39 (2023) 91–121.","chicago":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2023. https://doi.org/10.1146/annurev-cellbio-020823-011522.","ama":"Kicheva A, Briscoe J. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 2023;39:91-121. doi:10.1146/annurev-cellbio-020823-011522","ista":"Kicheva A, Briscoe J. 2023. Control of tissue development by morphogens. Annual Review of Cell and Developmental Biology. 39, 91–121.","mla":"Kicheva, Anna, and James Briscoe. “Control of Tissue Development by Morphogens.” Annual Review of Cell and Developmental Biology, vol. 39, Annual Reviews, 2023, pp. 91–121, doi:10.1146/annurev-cellbio-020823-011522.","ieee":"A. Kicheva and J. Briscoe, “Control of tissue development by morphogens,” Annual Review of Cell and Developmental Biology, vol. 39. Annual Reviews, pp. 91–121, 2023."},"date_published":"2023-10-16T00:00:00Z","year":"2023","intvolume":" 39","pmid":1,"page":"91-121","file":[{"creator":"dernst","file_id":"14491","date_updated":"2023-11-06T09:47:50Z","file_name":"2023_AnnualReviews_Kicheva.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"file_size":434819,"relation":"main_file","date_created":"2023-11-06T09:47:50Z","checksum":"461726014cf5907010afbd418d3c13ec"}],"ddc":["570"],"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Annual Review of Cell and Developmental Biology","status":"public","date_created":"2023-11-05T23:00:53Z","scopus_import":"1","type":"journal_article","acknowledgement":"We are grateful to Zena Hadjivasiliou for comments on this article. A.K. is supported by grants from the European Research Council under the European Union (EU) Horizon 2020 research and innovation program (680037) and Horizon Europe (101044579), and the Austrian Science Fund (F78) (Stem Cell Modulation). J.B. is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051), and by a grant from the European Research Council under the EU Horizon 2020 research and innovation program (742138).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"file_date_updated":"2023-11-06T09:47:50Z","corr_author":"1","_id":"14484","oa":1}]