[{"abstract":[{"text":"Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense.","lang":"eng"}],"type":"dissertation","_id":"19993","author":[{"full_name":"Strahodinsky, Florian","id":"979E35EE-C996-11E9-8C7C-CF13E6697425","last_name":"Strahodinsky","first_name":"Florian"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"page":"138","acknowledged_ssus":[{"_id":"LifeSc"}],"file":[{"embargo_to":"open_access","date_created":"2025-07-14T13:18:37Z","file_size":9857392,"date_updated":"2026-01-15T23:30:03Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"fstrahod","checksum":"df3a02f0d937ea9a3d79d5fb94fff097","file_id":"20021","relation":"source_file","file_name":"Thesis_Florian_Strahodinsky_DOCX.docx"},{"checksum":"7164c21fe1946e839f7b8acd255ce803","creator":"fstrahod","file_size":6439602,"date_updated":"2026-01-15T23:30:03Z","content_type":"application/pdf","access_level":"open_access","date_created":"2025-07-14T13:18:38Z","relation":"main_file","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf","embargo":"2026-01-15","file_id":"20022"}],"file_date_updated":"2026-01-15T23:30:03Z","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-19993","month":"07","day":"11","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.15479/AT-ISTA-19993","date_published":"2025-07-11T00:00:00Z","title":"Social immunity in a tri-partite host-pathogen relationship","corr_author":"1","date_updated":"2026-04-07T12:39:58Z","supervisor":[{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"ddc":["570"],"date_created":"2025-07-10T14:12:20Z","oa_version":"Published Version","citation":{"short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025.","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>.","ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"year":"2025","degree_awarded":"PhD","OA_place":"publisher","status":"public"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"113","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-059-6"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process."}],"type":"dissertation","OA_embargo":"12","_id":"19722","author":[{"orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","last_name":"Inumella"}],"acknowledgement":"Special thanks to the Plant Facility.","day":"23","month":"05","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publication_status":"published","file":[{"embargo":"2026-05-23","file_id":"19757","file_name":"Final Thesis_Syamala Inumella.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2026-05-23T22:30:02Z","file_size":8292363,"date_created":"2025-05-28T11:59:11Z","creator":"sinumell","checksum":"847ec70b2e40f50e0ddc7b8da201d52c"},{"relation":"source_file","file_name":"Final Thesis_Syamala Inumella.docx","file_id":"19758","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","creator":"sinumell","date_created":"2025-05-28T11:59:11Z","embargo_to":"open_access","file_size":7145703,"date_updated":"2026-05-23T22:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"file_date_updated":"2026-05-23T22:30:02Z","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-19722","doi":"10.15479/AT-ISTA-19722","date_published":"2025-05-23T00:00:00Z","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","corr_author":"1","date_updated":"2026-06-12T08:34:29Z","supervisor":[{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"ddc":["580"],"oa_version":"Published Version","date_created":"2025-05-23T15:21:29Z","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","year":"2025","degree_awarded":"PhD","OA_place":"publisher","status":"public","citation":{"ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria.","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>.","short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","mla":"Inumella, Syamala. <i>Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>","apa":"Inumella, S. (2025). <i>Molecular mechanisms of microtubule reorganization in elongating root epidermal cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>"},"alternative_title":["ISTA Thesis"]},{"fulldoi":"https://doi.org/10.15479/AT-ISTA-20470","article_processing_charge":"No","oa":1,"file":[{"creator":"brwu","checksum":"d32ea83f259f6b0506325cd57b1d44c3","date_updated":"2026-04-30T22:30:02Z","file_size":10603235,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-10-21T17:33:27Z","embargo_to":"open_access","relation":"source_file","file_name":"2025_Wu_Bryan_Thesis.docx","file_id":"20516"},{"date_created":"2025-10-21T17:33:26Z","date_updated":"2026-04-30T22:30:02Z","file_size":6251936,"access_level":"open_access","content_type":"application/pdf","creator":"brwu","checksum":"53590046fd3244c5550b4022282449d2","file_id":"20517","embargo":"2026-04-30","relation":"main_file","file_name":"2025_Wu_Bryan_Thesis.pdf"}],"file_date_updated":"2026-04-30T22:30:02Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"has_accepted_license":"1","month":"10","day":"30","author":[{"full_name":"Wu, Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","last_name":"Wu","first_name":"Bryan"}],"_id":"20470","type":"dissertation","abstract":[{"text":"Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems.","lang":"eng"}],"page":"102","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"citation":{"ista":"Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria.","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","mla":"Wu, Bryan. <i>An Examination on Phages as a Naturally Composable System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>.","chicago":"Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>.","short":"B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025.","apa":"Wu, B. (2025). <i>An examination on phages as a naturally composable system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>","ama":"Wu B. An examination on phages as a naturally composable system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>"},"status":"public","OA_place":"publisher","degree_awarded":"PhD","year":"2025","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"date_created":"2025-10-15T13:30:21Z","oa_version":"Published Version","ddc":["579"],"supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"date_updated":"2026-05-06T08:01:28Z","corr_author":"1","title":"An examination on phages as a naturally composable system","date_published":"2025-10-30T00:00:00Z","doi":"10.15479/AT-ISTA-20470"},{"alternative_title":["ISTA Thesis"],"citation":{"ista":"Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria.","ieee":"P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025.","mla":"Zivadinovic, Predrag. <i>Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>.","short":"P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025.","chicago":"Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>.","apa":"Zivadinovic, P. (2025). <i>Scale-free activity as a basis for spatial learning and memory in the brain</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>","ama":"Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>"},"status":"public","OA_place":"publisher","degree_awarded":"PhD","year":"2025","das_tickbox":"1","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","ddc":["570","539","571"],"date_updated":"2026-07-24T08:14:37Z","supervisor":[{"last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"project":[{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"}],"date_created":"2025-12-10T19:37:41Z","oa_version":"Published Version","date_published":"2025-12-11T00:00:00Z","doi":"10.15479/AT-ISTA-20777","corr_author":"1","title":"Scale-free activity as a basis for spatial learning and memory in the brain","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20777","oa":1,"file":[{"file_name":"2025_Zivadinovic_Predrag_PhD_thesis.pdf","relation":"main_file","file_id":"20778","embargo":"2026-06-11","creator":"pzivadin","checksum":"aae9d1ed53f7b67f75e289c26a02b72f","date_created":"2025-12-10T19:28:20Z","access_level":"open_access","content_type":"application/pdf","file_size":8105379,"date_updated":"2026-06-11T22:30:02Z"},{"checksum":"8a08a3804ce7d9d625fdf1631113da8c","creator":"pzivadin","embargo_to":"open_access","date_created":"2025-12-10T19:28:10Z","content_type":"application/zip","access_level":"closed","file_size":8512240,"date_updated":"2026-06-11T22:30:02Z","file_name":"2025_Zivadinovic_Predrag_PhD_thesis_source.zip","relation":"source_file","file_id":"20779"}],"file_date_updated":"2026-06-11T22:30:02Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"has_accepted_license":"1","month":"12","day":"11","author":[{"first_name":"Predrag","last_name":"Zivadinovic","full_name":"Zivadinovic, Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425"}],"_id":"20777","acknowledgement":"My work has been funded through the project \"Functional Advantages of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the FWF.\r\n","doi_confirm":"1","abstract":[{"text":"A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n","lang":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"104","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"corr_author":"1","title":"Exchange anisotropies in microwave-driven singlet-triplet qubits","APC_amount":"7068 EUR","external_id":{"arxiv":["2408.03224"],"isi":["001475587400022"],"pmid":["40274808"]},"doi":"10.1038/s41467-025-58969-y","date_published":"2025-04-24T00:00:00Z","date_created":"2025-03-19T13:28:12Z","oa_version":"Published Version","project":[{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"},{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"pmid":1,"date_updated":"2026-11-04T23:30:52Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"publisher":"Springer Nature","related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-shadow-of-an-electron/","description":"News on ISTA website","relation":"research_data"}],"record":[{"status":"public","id":"19409","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"19836"}]},"OA_type":"gold","OA_place":"publisher","year":"2025","quality_controlled":"1","status":"public","citation":{"ieee":"J. Saez Mollejo <i>et al.</i>, “Exchange anisotropies in microwave-driven singlet-triplet qubits,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","mla":"Saez Mollejo, Jaime, et al. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>, vol. 16, 3862, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>.","chicago":"Saez Mollejo, Jaime, Daniel Jirovec, Yona A Schell, Josip Kukucka, Stefano Calcaterra, Daniel Chrastina, Giovanni Isella, Maximilian Rimbach-Russ, Stefano Bosco, and Georgios Katsaros. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>.","short":"J. Saez Mollejo, D. Jirovec, Y.A. Schell, J. Kukucka, S. Calcaterra, D. Chrastina, G. Isella, M. Rimbach-Russ, S. Bosco, G. Katsaros, Nature Communications 16 (2025).","apa":"Saez Mollejo, J., Jirovec, D., Schell, Y. A., Kukucka, J., Calcaterra, S., Chrastina, D., … Katsaros, G. (2025). Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>","ama":"Saez Mollejo J, Jirovec D, Schell YA, et al. Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>","ista":"Saez Mollejo J, Jirovec D, Schell YA, Kukucka J, Calcaterra S, Chrastina D, Isella G, Rimbach-Russ M, Bosco S, Katsaros G. 2025. Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. 16, 3862."},"intvolume":"        16","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_identifier":{"eissn":["2041-1723"]},"volume":16,"type":"journal_article","abstract":[{"text":"Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime\r\nis strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors.","lang":"eng"}],"arxiv":1,"acknowledgement":"We thank A. Crippa for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project and the FWF Projects with DOI:10.55776/F86 and DOI:10.55776/I5060. M.R.-R. acknowledges support from the Netherlands Organization of Scientific Research (NWO) under Veni grant VI.Veni.212.223. The\r\nResearch of S.B. and M.R.-R. was sponsored in part by the Army Research Office and was accomplished under Award Number: W911NF-23-1-0110. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein.","_id":"19424","author":[{"first_name":"Jaime","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"last_name":"Jirovec","first_name":"Daniel","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"first_name":"Yona A","last_name":"Schell","id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5","full_name":"Schell, Yona A"},{"last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Rimbach-Russ, Maximilian","last_name":"Rimbach-Russ","first_name":"Maximilian"},{"first_name":"Stefano","last_name":"Bosco","full_name":"Bosco, Stefano"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"month":"04","day":"24","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GeKa"}],"file_date_updated":"2025-05-05T07:08:23Z","file":[{"date_created":"2025-05-05T07:08:23Z","access_level":"open_access","content_type":"application/pdf","file_size":1548756,"date_updated":"2025-05-05T07:08:23Z","checksum":"13fe84cddc9d4e47213bf17acdac70d7","creator":"dernst","file_id":"19645","success":1,"file_name":"2025_NatureComm_SaezMollejo.pdf","relation":"main_file"}],"oa":1,"article_type":"original","article_number":"3862","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41467-025-58969-y","article_processing_charge":"Yes","publication":"Nature Communications","isi":1},{"month":"06","day":"13","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publication_status":"published","file":[{"embargo_to":"open_access","date_created":"2025-06-16T09:38:49Z","file_size":59892829,"date_updated":"2026-04-01T22:30:07Z","content_type":"application/x-zip-compressed","access_level":"closed","checksum":"643bfddead59857536cce4d57c775b32","creator":"jsaezmol","file_id":"19849","relation":"source_file","file_name":"istaustriathesis-master - Copy.zip"},{"date_created":"2025-06-18T08:50:16Z","access_level":"open_access","content_type":"application/pdf","file_size":22382376,"date_updated":"2026-04-01T22:30:07Z","creator":"jsaezmol","checksum":"e3dcb767fcc2b1787a455fdda991cefb","file_id":"19851","embargo":"2026-04-01","file_name":"SaezMollejo_PhDFinal_pdfa-1b.pdf","relation":"main_file"}],"file_date_updated":"2026-04-01T22:30:07Z","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-19836","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"page":"175","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n"}],"type":"dissertation","doi_confirm":"1","_id":"19836","author":[{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"}],"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n","degree_awarded":"PhD","year":"2025","OA_place":"publisher","status":"public","citation":{"ista":"Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria.","ama":"Saez Mollejo J. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>","apa":"Saez Mollejo, J. (2025). <i>Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>","short":"J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.","chicago":"Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>.","mla":"Saez Mollejo, Jaime. <i>Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>.","ieee":"J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025."},"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT-ISTA-19836","date_published":"2025-06-13T00:00:00Z","corr_author":"1","title":"Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ","supervisor":[{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"date_updated":"2026-07-29T12:55:59Z","ddc":["530","539"],"oa_version":"Published Version","date_created":"2025-06-13T09:01:50Z","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology","grant_number":"101069515"},{"grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"relation":"part_of_dissertation","id":"19424","status":"public"}]}},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"10299","status":"public"}]},"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"supervisor":[{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-07-29T12:55:31Z","ddc":["530"],"date_created":"2025-06-26T08:39:08Z","oa_version":"Published Version","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.15479/AT-ISTA-19906","date_published":"2025-06-26T00:00:00Z","title":"Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ista":"Suresh SS. 2025. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria.","ieee":"S. S. Suresh, “Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote,” Institute of Science and Technology Austria, 2025.","mla":"Suresh, Sarath S. <i>Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>.","short":"S.S. Suresh, Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and Technology Austria, 2025.","chicago":"Suresh, Sarath S. “Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>.","apa":"Suresh, S. S. (2025). <i>Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>","ama":"Suresh SS. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>"},"ec_funded":1,"status":"public","OA_place":"publisher","year":"2025","degree_awarded":"PhD","doi_confirm":"1","acknowledgement":"This work was partially funded by the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo. 665385.","_id":"19906","author":[{"first_name":"Sarath S","last_name":"Suresh","full_name":"Suresh, Sarath S","id":"3D126CC4-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Flows of ordinary fluids such as water or air transition from laminar to turbulent\r\nmotion as the velocity increases. This simple dependence of the flow state\r\nsolely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here\r\nvarious different instabilities and turbulent states can arise at low and even\r\nvanishing inertia, while high inertia turbulence counterintuitively is suppressed\r\nand its drag strongly reduced. We here show in experiments of a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia, all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases of flow at high polymer concentrations, exploring the\r\nrelationship between flow at these wide range of control parameters.\r\n","lang":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"82","acknowledged_ssus":[{"_id":"M-Shop"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-19906","file_date_updated":"2025-12-27T23:30:02Z","file":[{"file_id":"19907","embargo":"2025-12-27","relation":"main_file","file_name":"Thesis_v9_PDFA2b.pdf","date_created":"2025-06-26T08:40:53Z","file_size":6504571,"date_updated":"2025-12-27T23:30:02Z","content_type":"application/pdf","access_level":"open_access","checksum":"302a07605a9e64ac247c2036d5f5b1cd","creator":"cchlebak"},{"file_id":"19908","relation":"source_file","file_name":"Thesis Template - ISTA [istaustriathesis].zip","date_updated":"2025-12-27T23:30:02Z","file_size":59092991,"content_type":"application/x-zip-compressed","access_level":"closed","date_created":"2025-06-26T08:41:24Z","embargo_to":"open_access","creator":"cchlebak","checksum":"5d69d10bdacc24c27f02924379405bd9"}],"oa":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"month":"06","day":"26","has_accepted_license":"1"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"12248","status":"public"},{"status":"public","id":"10767","relation":"part_of_dissertation"},{"status":"public","id":"14613","relation":"part_of_dissertation"},{"id":"10167","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"15009","status":"public"},{"id":"17890","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570","576"],"date_updated":"2026-09-24T11:17:37Z","supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"oa_version":"Published Version","date_created":"2025-03-11T12:54:31Z","date_published":"2025-03-14T00:00:00Z","doi":"10.15479/AT-ISTA-19386","corr_author":"1","title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","alternative_title":["ISTA Thesis"],"citation":{"ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria."},"status":"public","degree_awarded":"PhD","OA_place":"publisher","year":"2025","OA_embargo":"12","acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","_id":"19386","author":[{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"abstract":[{"text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. ","lang":"eng"}],"type":"dissertation","page":"170","publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-19386","oa":1,"file":[{"file_name":"Thesis_Marwan_Elkrewi.docx","relation":"source_file","file_id":"19462","checksum":"5549a8216c07e4c39281648912d72246","creator":"melkrewi","date_created":"2025-03-26T07:06:56Z","embargo_to":"open_access","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25019680,"date_updated":"2026-03-26T23:30:03Z"},{"file_id":"19463","embargo":"2026-03-26","relation":"main_file","file_name":"Thesis_Marwan_Elkrewi.pdf","date_created":"2025-03-26T07:06:22Z","file_size":17294844,"date_updated":"2026-03-26T23:30:03Z","access_level":"open_access","content_type":"application/pdf","checksum":"aed2ba9965aa89b3414deae1ae9f4321","creator":"melkrewi"}],"file_date_updated":"2026-03-26T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","has_accepted_license":"1","day":"14","month":"03"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"114","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Males and females of many  species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria  ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. ","lang":"eng"}],"type":"dissertation","_id":"20449","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","author":[{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"}],"month":"10","day":"10","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publication_status":"published","file":[{"date_created":"2025-10-20T13:32:29Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2026-06-01T22:30:04Z","file_size":18507283,"checksum":"26905c22bca417198a733d792d8ce422","creator":"vbett","file_id":"20507","embargo":"2026-06-01","file_name":"2025_Bett_Vincent_Thesis.pdf","relation":"main_file"},{"file_name":"2025_Bett_Vincent_Thesis.docx","relation":"source_file","file_id":"20508","creator":"vbett","checksum":"6a09a8d126d3628bfd8a35202735f267","embargo_to":"open_access","date_created":"2025-10-20T13:35:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2026-06-01T22:30:04Z","file_size":17163921}],"file_date_updated":"2026-06-01T22:30:04Z","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20449","doi":"10.15479/AT-ISTA-20449","date_published":"2025-10-10T00:00:00Z","corr_author":"1","title":"Evolution and regulation of the Z chromosome","supervisor":[{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"date_updated":"2026-09-24T11:11:01Z","ddc":["576"],"date_created":"2025-10-11T08:18:51Z","oa_version":"Published Version","project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"19735","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"15009","status":"public"}]},"year":"2025","OA_place":"publisher","degree_awarded":"PhD","status":"public","citation":{"ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","chicago":"Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","apa":"Bett, V. K. (2025). <i>Evolution and regulation of the Z chromosome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>","ama":"Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>","ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"]},{"OA_place":"publisher","year":"2025","OA_type":"gold","quality_controlled":"1","status":"public","citation":{"ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>"},"intvolume":"        42","DOAJ_listed":"1","corr_author":"1","external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","date_published":"2025-05-01T00:00:00Z","doi":"10.1093/molbev/msaf085","project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"oa_version":"Published Version","date_created":"2025-05-25T22:16:56Z","ddc":["570"],"pmid":1,"date_updated":"2026-11-04T23:31:05Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Oxford University Press","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git","relation":"software"}],"record":[{"id":"20449","relation":"dissertation_contains","status":"public"},{"status":"deleted","id":"20444","relation":"dissertation_contains"}]},"has_accepted_license":"1","month":"05","day":"01","issue":"5","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"publication_status":"published","oa":1,"file_date_updated":"2025-05-28T09:34:36Z","file":[{"file_name":"2025_MBE_Bett.pdf","relation":"main_file","success":1,"file_id":"19756","checksum":"6c14b03f94b4aadf8869be2c4366d077","creator":"dernst","date_created":"2025-05-28T09:34:36Z","content_type":"application/pdf","access_level":"open_access","file_size":1282772,"date_updated":"2025-05-28T09:34:36Z"}],"article_number":"msaf085","article_type":"original","fulldoi":"https://doi.org/10.1093/molbev/msaf085","scopus_import":"1","isi":1,"publication":"Molecular Biology and Evolution","article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"ScienComp"}],"volume":42,"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"type":"journal_article","abstract":[{"text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.","lang":"eng"}],"author":[{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"},{"full_name":"Trejo Arellano, Minerva S","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","orcid":"0000-0002-1982-3475","first_name":"Minerva S","last_name":"Trejo Arellano"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"_id":"19735","acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA."},{"citation":{"ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025.","mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"year":"2025","OA_place":"publisher","degree_awarded":"PhD","status":"public","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18525"}]},"date_published":"2025-09-15T00:00:00Z","doi":"10.15479/AT-ISTA-20357","title":"Effect propagation in biological networks","corr_author":"1","ddc":["570","530"],"date_updated":"2026-10-02T10:15:31Z","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"date_created":"2025-09-15T17:04:48Z","oa_version":"Published Version","oa":1,"file_date_updated":"2026-09-15T22:30:02Z","file":[{"date_created":"2026-08-07T10:57:05Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","access_level":"closed","file_size":56464803,"date_updated":"2026-09-15T22:30:02Z","checksum":"0582508d439b233497384f83a8307398","creator":"cchlebak","file_id":"22661","file_name":"2025_Ruzickova_Natalia_Thesis.zip","relation":"source_file"},{"file_id":"22662","embargo":"2026-09-15","relation":"main_file","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","date_created":"2026-08-07T10:57:34Z","file_size":30634378,"date_updated":"2026-09-15T22:30:02Z","content_type":"application/pdf","access_level":"open_access","checksum":"b722289fd550abede63adc27b9c61784","creator":"cchlebak"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20357","has_accepted_license":"1","day":"15","month":"09","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"type":"dissertation","_id":"20357","author":[{"first_name":"Natalia","last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"}],"acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","doi_confirm":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-066-4"],"issn":["2663-337X"]},"page":"156","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}]},{"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20563","file":[{"file_name":"2025_quattrocchi_filippo_thesis.pdf","relation":"main_file","embargo":"2026-01-01","file_id":"20653","creator":"fquattro","checksum":"6f55275bdf99992be3a6457d949dd664","content_type":"application/pdf","access_level":"open_access","date_updated":"2026-01-01T23:30:03Z","file_size":4326411,"date_created":"2025-11-17T21:04:15Z"},{"creator":"fquattro","checksum":"707e580f5d993a214c0dba456b75837b","file_size":11726509,"date_updated":"2026-01-01T23:30:03Z","access_level":"closed","content_type":"application/zip","embargo_to":"open_access","date_created":"2025-11-17T21:05:43Z","relation":"source_file","file_name":"2025_quattrocchi_thesis.zip","file_id":"20654"}],"file_date_updated":"2026-01-01T23:30:03Z","oa":1,"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publication_status":"published","month":"11","day":"03","has_accepted_license":"1","_id":"20563","author":[{"full_name":"Quattrocchi, Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","first_name":"Filippo"}],"acknowledgement":"The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65.","abstract":[{"text":"The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n","lang":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"page":"240","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ista":"Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria.","ama":"Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>","apa":"Quattrocchi, F. (2025). <i>Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>","chicago":"Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>.","short":"F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025.","ieee":"F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025.","mla":"Quattrocchi, Filippo. <i>Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>."},"status":"public","degree_awarded":"PhD","OA_place":"publisher","year":"2025","related_material":{"record":[{"relation":"part_of_dissertation","id":"20569","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"20571"},{"status":"public","relation":"part_of_dissertation","id":"20570"},{"id":"18706","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-10-02T11:24:55Z","supervisor":[{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"}],"ddc":["515","519"],"date_created":"2025-10-28T13:10:49Z","oa_version":"Published Version","project":[{"grant_number":"F06504","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems"}],"keyword":["optimal transport","kinetic equations","boundary value problems","quantization","gradient flows","homogenization"],"doi":"10.15479/AT-ISTA-20563","date_published":"2025-11-03T00:00:00Z","title":"Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures","corr_author":"1"},{"year":"2025","OA_place":"repository","OA_type":"green","status":"public","ec_funded":1,"citation":{"short":"G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.).","chicago":"Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>.","ieee":"G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” <i>arXiv</i>. .","mla":"Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, 2502.15665, doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>.","ama":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>","apa":"Brigati, G., Maas, J., &#38; Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>","ista":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv, 2502.15665."},"date_published":"2025-08-10T00:00:00Z","doi":"10.48550/arXiv.2502.15665","corr_author":"1","title":"Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures","external_id":{"arxiv":["2502.15665"]},"date_updated":"2026-11-04T23:31:11Z","keyword":["optimal transport","kinetic theory","second-order discrepancy","Vlasov equation","Wasserstein splines."],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"oa_version":"Preprint","date_created":"2025-10-28T13:12:08Z","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"20563","relation":"dissertation_contains"}]},"day":"10","month":"08","publication_status":"draft","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"article_number":"2502.15665","oa":1,"publication":"arXiv","article_processing_charge":"No","fulldoi":"https://doi.org/10.48550/arXiv.2502.15665","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2502.15665","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves."}],"type":"preprint","_id":"20569","author":[{"last_name":"Brigati","first_name":"Giovanni","full_name":"Brigati, Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1"},{"last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"},{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","first_name":"Filippo"}],"acknowledgement":"This work was partially inspired by an unpublished note from 2014 by Guillaume Carlier,\r\nJean Dolbeault, and Bruno Nazaret. GB deeply thanks Jean Dolbeault for proposing\r\nthis problem to him, guiding him into the subject, and sharing the aforementioned note.\r\nWe are grateful to Karthik Elamvazhuthi for making us aware of the work [20].\r\nThe work of GB has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo 101034413.\r\nJM and FQ gratefully acknowledge support from the Austrian Science Fund (FWF)\r\nproject 10.55776/F65.","arxiv":1},{"ec_funded":1,"status":"public","degree_awarded":"PhD","year":"2025","OA_place":"publisher","alternative_title":["ISTA Thesis"],"citation":{"ista":"Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria.","ama":"Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>","apa":"Sett, R. (2025). <i>Quantum remote sensing and non-equilibrium phase transitions in the microwave regime</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>","short":"R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","chicago":"Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>.","mla":"Sett, Riya. <i>Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>.","ieee":"R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025."},"oa_version":"Published Version","date_created":"2025-04-09T16:44:26Z","keyword":["phase transition","open quantum system","phase diagram","cavity quantum electrodynamics","superconducting qubits","semiclassical physics","quantum optics","josephson junction","parametric converter","phase conjugation","quantum radar","quantum entanglement","correlation","quantum sensing"],"project":[{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"date_updated":"2026-10-15T09:08:00Z","supervisor":[{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"ddc":["530"],"title":"Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","corr_author":"1","doi":"10.15479/AT-ISTA-19533","date_published":"2025-04-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"18978"},{"status":"public","relation":"part_of_dissertation","id":"19280"},{"relation":"part_of_dissertation","id":"13117","status":"public"},{"relation":"part_of_dissertation","id":"17183","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_status":"published","month":"04","day":"1","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT-ISTA-19533","article_processing_charge":"No","file":[{"checksum":"ba6cd2289d0141a160a14fc97df1632f","creator":"rsett","date_created":"2025-04-10T11:33:22Z","date_updated":"2025-10-11T22:30:02Z","file_size":4129208,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","file_id":"19538","embargo":"2025-10-11"},{"file_id":"19539","relation":"source_file","file_name":"PhD Thesis Riya Sett.zip","file_size":6646110,"date_updated":"2025-10-11T22:30:02Z","content_type":"application/x-zip-compressed","access_level":"closed","embargo_to":"open_access","date_created":"2025-04-10T11:34:08Z","creator":"rsett","checksum":"ee63a94cb8f7adf5e766903028b81ed6"}],"file_date_updated":"2025-10-11T22:30:02Z","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"publication_identifier":{"issn":["2663-337X"]},"page":"109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi_confirm":"1","_id":"19533","acknowledgement":"I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work.","author":[{"first_name":"Riya","last_name":"Sett","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","abstract":[{"text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n","lang":"eng"}]},{"citation":{"ista":"Redchenko E, Zens M, Zemlicka M, Peruzzo M, Hassani F, Sett R, Zielinski PD, Dhar HS, Krimer DO, Rotter S, Fink JM. 2025. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 134(6), 063601.","apa":"Redchenko, E., Zens, M., Zemlicka, M., Peruzzo, M., Hassani, F., Sett, R., … Fink, J. M. (2025). Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>","ama":"Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. <i>Physical Review Letters</i>. 2025;134(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>","ieee":"E. Redchenko <i>et al.</i>, “Observation of collapse and revival in a superconducting atomic frequency comb,” <i>Physical Review Letters</i>, vol. 134, no. 6. American Physical Society, 2025.","mla":"Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">10.1103/PhysRevLett.134.063601</a>.","short":"E. Redchenko, M. Zens, M. Zemlicka, M. Peruzzo, F. Hassani, R. Sett, P.D. Zielinski, H.S. Dhar, D.O. Krimer, S. Rotter, J.M. Fink, Physical Review Letters 134 (2025).","chicago":"Redchenko, Elena, M. Zens, Martin Zemlicka, Matilda Peruzzo, Farid Hassani, Riya Sett, Przemyslaw D Zielinski, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.063601\">https://doi.org/10.1103/PhysRevLett.134.063601</a>."},"intvolume":"       134","OA_type":"hybrid","year":"2025","OA_place":"publisher","ec_funded":1,"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"American Physical Society","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"19533","relation":"dissertation_contains","status":"public"}]},"doi":"10.1103/PhysRevLett.134.063601","date_published":"2025-02-14T00:00:00Z","external_id":{"pmid":["40021171"],"isi":["001454696700003"],"arxiv":["2310.04200"]},"corr_author":"1","title":"Observation of collapse and revival in a superconducting atomic frequency comb","date_updated":"2026-11-04T23:31:12Z","pmid":1,"ddc":["530"],"oa_version":"Published Version","date_created":"2025-03-02T23:01:52Z","project":[{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"},{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"}],"article_type":"original","article_number":"063601","file":[{"success":1,"file_id":"19291","relation":"main_file","file_name":"2025_PhysReviewLetters_Redchenko.pdf","date_created":"2025-03-04T10:40:50Z","date_updated":"2025-03-04T10:40:50Z","file_size":2080408,"content_type":"application/pdf","access_level":"open_access","checksum":"633d6c5ddd9b805da22c5839d3d48df6","creator":"dernst"}],"file_date_updated":"2025-03-04T10:40:50Z","oa":1,"article_processing_charge":"Yes (via OA deal)","publication":"Physical Review Letters","isi":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1103/PhysRevLett.134.063601","day":"14","month":"02","has_accepted_license":"1","department":[{"_id":"JoFi"}],"publication_status":"published","issue":"6","abstract":[{"lang":"eng","text":"Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics."}],"type":"journal_article","arxiv":1,"author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Zens, M.","first_name":"M.","last_name":"Zens"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032"},{"last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628"},{"first_name":"Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett"},{"last_name":"Zielinski","first_name":"Przemyslaw D","id":"e198fcc4-f6e0-11ea-865d-b6a256760ee8","full_name":"Zielinski, Przemyslaw D"},{"first_name":"H. S.","last_name":"Dhar","full_name":"Dhar, H. S."},{"last_name":"Krimer","first_name":"D. O.","full_name":"Krimer, D. O."},{"last_name":"Rotter","first_name":"S.","full_name":"Rotter, S."},{"first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"_id":"19280","acknowledgement":"The authors thank G. Arnold and R. Sahu for the discussions, L. Drmic for software development, the MIBA workshop and the ISTA nanofabrication facility for technical support, and VTT Technical Research Centre of Finland for providing us TWPAs for follow-up measurements. This work was supported by the Austrian Science Fund (FWF) [Grant DOI: 10.55776/F71] through BeyondC (F7105) and IST Austria. E. S. R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J. M. F. and M. Ž. acknowledge support from the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"volume":134,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20212","oa":1,"file":[{"file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx","relation":"source_file","file_id":"20230","creator":"omiranda","checksum":"3331f76bbef74ff4908e2d2c9262045c","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":32887334,"date_updated":"2026-08-26T22:30:02Z","date_created":"2025-08-26T09:03:50Z","embargo_to":"open_access"},{"relation":"main_file","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","file_id":"20231","embargo":"2026-08-26","checksum":"02509d50cff8e35c5bcbf71e8d658176","creator":"omiranda","date_created":"2025-08-26T09:05:55Z","date_updated":"2026-08-26T22:30:02Z","file_size":28636240,"content_type":"application/pdf","access_level":"open_access"}],"file_date_updated":"2026-08-26T22:30:02Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publication_status":"published","has_accepted_license":"1","day":"22","month":"08","acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","_id":"20212","author":[{"orcid":"0000-0001-6618-6889","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","last_name":"Miranda","first_name":"Osvaldo"}],"doi_confirm":"1","abstract":[{"text":"Cortical development has been studied for many decades and with each passing year, we learn \r\nmore about the processes that govern the tightly regulated developmental program. Up until \r\nrecently, the field has struggled to gain reliable access to progenitors at the single-cell level, \r\nlimiting the resolution at which we can study cortical development in vivo. Therefore, much of \r\nthe data we have on mammalian cortical development is at the cell population level. The \r\nsubsequent pages of this thesis describe novel elements of cortical development in mice; \r\nacquired using a candidate gene approach in conjunction with Mosaic Analysis with Double \r\nMarkers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview \r\nof the state of the field, describe the methodology used to quantify morphological \r\ncharacteristics of neurons and glia, and delve into the role of Phosphatase and tensin \r\nhomologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse \r\ncortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells \r\nare mutated, to study population-level changes, we can bypass the early postnatal lethality \r\nreported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to \r\ninduce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor \r\nlevel. Pten-mutant neuron populations within the mosaics were significantly expanded. In the \r\nlatter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance \r\nof astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate \r\nPten mosaics within a series of distinct knockout tissues to test for the interactions between \r\nPten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey \r\nof Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical \r\neffectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results \r\ndemonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage \r\nprogression. ","lang":"eng"}],"type":"dissertation","publication_identifier":{"isbn":["978-3-99078-063-3"],"issn":["2663-337X"]},"page":"119","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"citation":{"ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>","ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria."},"status":"public","year":"2025","degree_awarded":"PhD","OA_place":"publisher","related_material":{"record":[{"id":"17425","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"supervisor":[{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"date_updated":"2026-10-02T12:16:56Z","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253"}],"keyword":["Pten","mtor","cortical development","MADM","Mapk"],"date_created":"2025-08-22T14:07:00Z","oa_version":"Published Version","date_published":"2025-08-22T00:00:00Z","doi":"10.15479/AT-ISTA-20212","corr_author":"1","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM"},{"OA_place":"publisher","degree_awarded":"PhD","year":"2025","status":"public","citation":{"chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","mla":"Wang, Yiqun. <i>The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20117\">10.15479/AT-ISTA-20117</a>","apa":"Wang, Y. (2025). <i>The role of dynamin related protein 2A in cytokinin regulated plant growth and development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20117\">https://doi.org/10.15479/AT-ISTA-20117</a>","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT-ISTA-20117","date_published":"2025-08-04T00:00:00Z","corr_author":"1","title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","supervisor":[{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"date_updated":"2026-10-02T12:33:36Z","ddc":["580"],"date_created":"2025-08-04T15:24:21Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18063"}]},"day":"04","month":"08","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file":[{"file_id":"20209","relation":"source_file","file_name":"2025_Wang_Yiqun_Thesis.docx","date_updated":"2026-09-03T22:30:03Z","file_size":25798848,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","date_created":"2025-08-22T08:22:10Z","creator":"yiqwang","checksum":"36b87c17d12c7bf5955d6d812acb8d77"},{"creator":"yiqwang","checksum":"8d7a2383f66377da675d379ec30ea0fe","date_created":"2025-08-22T10:32:30Z","date_updated":"2026-09-03T22:30:03Z","file_size":12628313,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2025_Wang_Yiqun_Thesis.pdf","file_id":"20211","embargo":"2026-09-03"}],"file_date_updated":"2026-09-03T22:30:03Z","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20117","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"page":"108","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Auxin is essential for many aspects of plant growth and development, from \r\nembryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and \r\ngradients, which are important for regulating various plant development process, including \r\nembryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is \r\nmediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The \r\nregulation of PIN proteins is a key convergence of crosstalk between auxin and other \r\nhormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis \r\nroots, preferentially the dephosphorylated PIN1, and the process is independent of \r\ntranscription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization \r\nof PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis \r\n(Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 \r\ndegradation through regulating the phosphorylation of PIN1 or trafficking components is \r\nunknown. Here, we demonstrate that dynamin related protein DRP2s are required for the \r\ncytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite \r\nthe reported redundancy of DRP2A and DRP2B in gametophyte development, we found that \r\nCK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a \r\nor drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of \r\nDRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma \r\nmembrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin \r\nreceptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly \r\ncycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we \r\ninvestigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in \r\ncytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN \r\ntrafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of \r\nendocytosis accessory protein DRP2A. "}],"type":"dissertation","doi_confirm":"1","author":[{"id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun","last_name":"Wang","first_name":"Yiqun"}],"_id":"20117","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments."},{"quality_controlled":"1","status":"public","OA_type":"hybrid","OA_place":"publisher","year":"2025","intvolume":"       123","citation":{"ista":"Babic D, Abualia R, Fiedler L, Qi L, Tellier F, Smoljan A, Rakusova H, Valošek P, Han H, Benková E, Faure JD, Friml J. 2025. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. Plant Journal. 123(3), e70396.","chicago":"Babic, David, Rashed Abualia, Lukas Fiedler, Linlin Qi, Frédérique Tellier, Adrijana Smoljan, Hana Rakusova, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>.","short":"D. Babic, R. Abualia, L. Fiedler, L. Qi, F. Tellier, A. Smoljan, H. Rakusova, P. Valošek, H. Han, E. Benková, J.D. Faure, J. Friml, Plant Journal 123 (2025).","ieee":"D. Babic <i>et al.</i>, “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” <i>Plant Journal</i>, vol. 123, no. 3. Wiley, 2025.","mla":"Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” <i>Plant Journal</i>, vol. 123, no. 3, e70396, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>.","ama":"Babic D, Abualia R, Fiedler L, et al. Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. 2025;123(3). doi:<a href=\"https://doi.org/10.1111/tpj.70396\">10.1111/tpj.70396</a>","apa":"Babic, D., Abualia, R., Fiedler, L., Qi, L., Tellier, F., Smoljan, A., … Friml, J. (2025). Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.70396\">https://doi.org/10.1111/tpj.70396</a>"},"date_updated":"2026-11-04T23:31:15Z","pmid":1,"ddc":["580"],"oa_version":"Published Version","date_created":"2025-08-17T22:01:36Z","project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"}],"doi":"10.1111/tpj.70396","date_published":"2025-08-01T00:00:00Z","external_id":{"pmid":["40782342"],"isi":["001547884300001"]},"corr_author":"1","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20362"}]},"publisher":"Wiley","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"publication_status":"published","issue":"3","day":"01","month":"08","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","isi":1,"publication":"Plant Journal","fulldoi":"https://doi.org/10.1111/tpj.70396","scopus_import":"1","article_type":"original","article_number":"e70396","file":[{"relation":"main_file","file_name":"2025_PlantJournal_Babic.pdf","success":1,"file_id":"20264","creator":"dernst","checksum":"1cdc3341d2d23101abca72521f1f23cb","file_size":5791111,"date_updated":"2025-09-01T14:09:31Z","access_level":"open_access","content_type":"application/pdf","date_created":"2025-09-01T14:09:31Z"}],"file_date_updated":"2025-09-01T14:09:31Z","oa":1,"publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"volume":123,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"20187","PlanS_conform":"1","acknowledgement":"We gratefully acknowledge the Imaging and Optics, Electron Microscopy (especially Vanessa Zheden for technical assistance) and Life Science (in particular Dorota Jaworska) facilities at ISTA for their continuous support. Authors would like to thank Michelle Gallei for advice during the generation of the transgenic lines; Zuzana Gelová for advice with DR5rev::GFP analyses; Ivan Kulich for help and advice on trichome imaging; Aline Monzer for generous help with hypocotyl and root analyses; Shutang Tan for help with the NGS data analysis; and Milan Župunski for advice on abiotic stress experiments. We would like to thank Dolf Weijers for the SOSEKI (SOK) marker line seeds. This work has benefited from the support of IJPB's Plant Observatory platforms P0-Chem.\r\n\r\nThis work was supported by Austrian Science Fund (FWF) (I 6123-B) and Science and Technology Department of Jiangxi Province (20223BCJ25037) to Huibin Han. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","author":[{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","full_name":"Babic, David","last_name":"Babic","first_name":"David"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","first_name":"Rashed","last_name":"Abualia"},{"full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler","first_name":"Lukas"},{"orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin"},{"full_name":"Tellier, Frédérique","first_name":"Frédérique","last_name":"Tellier"},{"id":"cced8a85-223e-11ed-af04-b0596c55053b","full_name":"Smoljan, Adrijana","last_name":"Smoljan","first_name":"Adrijana"},{"first_name":"Hana","last_name":"Rakusova","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","full_name":"Rakusova, Hana"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","full_name":"Valošek, Petr","first_name":"Petr","last_name":"Valošek"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"full_name":"Faure, Jean Denis","last_name":"Faure","first_name":"Jean Denis"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"abstract":[{"text":"Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.","lang":"eng"}],"type":"journal_article"},{"file_date_updated":"2026-09-25T22:30:02Z","file":[{"checksum":"5ecf274281a54a41e0288bc79edf7492","creator":"dbabic","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-09-25T22:30:02Z","file_size":7501548,"date_created":"2025-09-24T13:43:14Z","file_name":"2025_David_Babic_Thesis.pdf","relation":"main_file","embargo":"2026-09-25","file_id":"20388"},{"checksum":"2703e548390de0a1af7a707137e8ab3b","creator":"dbabic","date_created":"2025-09-24T13:43:14Z","embargo_to":"open_access","date_updated":"2026-09-25T22:30:02Z","file_size":23206052,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Babic_draft.docx","file_id":"20389"}],"oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-20362","month":"09","day":"18","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","abstract":[{"text":"Arabidopsis embryo has long served as a model system for understanding how plant body \r\npatterning and axis establishment arise. Previous work established that auxin flows, directed \r\nby polar transport and reinforced by local biosynthesis, underpin axes formation, while recent \r\nstudies suggest that maternal tissue, membrane composition and surface receptor signaling add \r\nfurther regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which \r\nguide plant embryonic and post-embryonic development. We review methodological advances \r\nthat allow the embryo to be imaged and studied. These tools offer exciting venues for future \r\naddressing of outstanding research questions. Furthermore, we dissect the contribution of \r\nmaternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments \r\nlowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens \r\nthe initial apical maximum. The resulting deficit dampens downstream embryonic auxin \r\nbiosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided \r\nauxin controls auxin flows in the embryos on a larger scale than previously understood. \r\nIntriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases \r\nTMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be \r\npreferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK \r\nactivity arrests embryos, affects seedling development and persists into adult growth, \r\nsuggesting that maternal effect could shape development beyond fertilization and early \r\nembryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane \r\ncomposition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid \r\nmetabolism triggers widespread patterning errors. \r\nTogether, these results reposition early plant patterning as a hierarchical cascade that begins \r\nwith maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated \r\nby maternal receptor signaling and could ultimately be gated by the biophysical properties of \r\nthe membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking \r\ninto a single narrative, this thesis helps shifting the approach of viewing the embryo as an \r\nautonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal \r\ncontext.","lang":"eng"}],"type":"dissertation","doi_confirm":"1","author":[{"last_name":"Babic","first_name":"David","full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7"}],"_id":"20362","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"page":"116","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"citation":{"ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025.","mla":"Babic, David. <i>Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>.","chicago":"Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","apa":"Babic, D. (2025). <i>Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20362\">https://doi.org/10.15479/AT-ISTA-20362</a>","ama":"Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20362\">10.15479/AT-ISTA-20362</a>","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"year":"2025","degree_awarded":"PhD","OA_place":"publisher","status":"public","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"20187","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT-ISTA-20362","date_published":"2025-09-18T00:00:00Z","title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","corr_author":"1","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"date_updated":"2026-10-16T07:59:32Z","ddc":["580"],"date_created":"2025-09-17T13:28:01Z","oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo."}],"type":"preprint","_id":"21427","acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","author":[{"full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","first_name":"Zuzana"},{"orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","first_name":"Saren","last_name":"Tasciyan"},{"first_name":"Juraj","last_name":"Majek","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"last_name":"Sahai","first_name":"Erik","full_name":"Sahai, Erik"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication":"bioRxiv","article_processing_charge":"No","fulldoi":"https://doi.org/10.1101/2025.05.20.655037","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"has_accepted_license":"1","day":"25","month":"09","publication_status":"draft","department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"das_tickbox":"1","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"related_material":{"record":[{"id":"21439","relation":"research_data","status":"public"},{"relation":"later_version","id":"22963","status":"public"},{"status":"public","id":"21423","relation":"dissertation_contains"}]},"date_published":"2025-09-25T00:00:00Z","doi":"10.1101/2025.05.20.655037","corr_author":"1","title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","ddc":["539","570"],"date_updated":"2026-11-04T23:31:15Z","project":[{"grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces"},{"grant_number":"26360","name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"oa_version":"Preprint","date_created":"2026-03-11T08:40:06Z","citation":{"apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>."},"year":"2025","OA_place":"repository","status":"public"}]