--- OA_place: publisher _id: '19993' abstract: - lang: eng 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." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florian full_name: Strahodinsky, Florian id: 979E35EE-C996-11E9-8C7C-CF13E6697425 last_name: Strahodinsky citation: ama: Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:10.15479/AT-ISTA-19993 apa: Strahodinsky, F. (2025). Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19993 chicago: Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19993. ieee: F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025. ista: Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. mla: Strahodinsky, Florian. Social Immunity in a Tri-Partite Host-Pathogen Relationship. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19993. short: F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-10T14:12:20Z date_published: 2025-07-11T00:00:00Z date_updated: 2026-04-07T12:39:58Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/AT-ISTA-19993 file: - access_level: closed checksum: df3a02f0d937ea9a3d79d5fb94fff097 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fstrahod date_created: 2025-07-14T13:18:37Z date_updated: 2026-01-15T23:30:03Z embargo_to: open_access file_id: '20021' file_name: Thesis_Florian_Strahodinsky_DOCX.docx file_size: 9857392 relation: source_file - access_level: open_access checksum: 7164c21fe1946e839f7b8acd255ce803 content_type: application/pdf creator: fstrahod date_created: 2025-07-14T13:18:38Z date_updated: 2026-01-15T23:30:03Z embargo: 2026-01-15 file_id: '20022' file_name: Thesis_Florian_Strahodinsky_PDF.pdf file_size: 6439602 relation: main_file file_date_updated: 2026-01-15T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19993 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '138' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Social immunity in a tri-partite host-pathogen relationship tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19722' 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." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: Special thanks to the Plant Facility. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Syamala full_name: Inumella, Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella orcid: 0009-0002-5890-120X citation: ama: Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722 apa: Inumella, S. (2025). Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19722 chicago: Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19722. ieee: S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025. ista: Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. mla: Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19722. short: S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-23T15:21:29Z date_published: 2025-05-23T00:00:00Z date_updated: 2026-06-12T08:34:29Z day: '23' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-19722 file: - access_level: open_access checksum: 847ec70b2e40f50e0ddc7b8da201d52c content_type: application/pdf creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo: 2026-05-23 file_id: '19757' file_name: Final Thesis_Syamala Inumella.pdf file_size: 8292363 relation: main_file - access_level: closed checksum: 17cdffdae13a5f65bdad9c84e9e0e3bd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo_to: open_access file_id: '19758' file_name: Final Thesis_Syamala Inumella.docx file_size: 7145703 relation: source_file file_date_updated: 2026-05-23T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19722 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '113' publication_identifier: isbn: - 978-3-99078-059-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of microtubule reorganization in elongating root epidermal cells type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20470' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bryan full_name: Wu, Bryan id: 3C521EBA-F248-11E8-B48F-1D18A9856A87 last_name: Wu citation: ama: Wu B. An examination on phages as a naturally composable system. 2025. doi:10.15479/AT-ISTA-20470 apa: Wu, B. (2025). An examination on phages as a naturally composable system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20470 chicago: Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20470. ieee: B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025. ista: Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria. mla: Wu, Bryan. An Examination on Phages as a Naturally Composable System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20470. short: B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-15T13:30:21Z date_published: 2025-10-30T00:00:00Z date_updated: 2026-05-06T08:01:28Z day: '30' ddc: - '579' degree_awarded: PhD department: - _id: GradSch - _id: CaGu doi: 10.15479/AT-ISTA-20470 file: - access_level: closed checksum: d32ea83f259f6b0506325cd57b1d44c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: brwu date_created: 2025-10-21T17:33:27Z date_updated: 2026-04-30T22:30:02Z embargo_to: open_access file_id: '20516' file_name: 2025_Wu_Bryan_Thesis.docx file_size: 10603235 relation: source_file - access_level: open_access checksum: 53590046fd3244c5550b4022282449d2 content_type: application/pdf creator: brwu date_created: 2025-10-21T17:33:26Z date_updated: 2026-04-30T22:30:02Z embargo: 2026-04-30 file_id: '20517' file_name: 2025_Wu_Bryan_Thesis.pdf file_size: 6251936 relation: main_file file_date_updated: 2026-04-30T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20470 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: An examination on phages as a naturally composable system type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20777' abstract: - lang: eng 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" 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Predrag full_name: Zivadinovic, Predrag id: 68AA0E5A-AFDA-11E9-9994-141DE6697425 last_name: Zivadinovic citation: ama: Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:10.15479/AT-ISTA-20777 apa: Zivadinovic, P. (2025). Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20777 chicago: Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20777. ieee: P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025. ista: Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. mla: Zivadinovic, Predrag. Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20777. short: P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-12-10T19:37:41Z date_published: 2025-12-11T00:00:00Z date_updated: 2026-07-24T08:14:37Z day: '11' ddc: - '570' - '539' - '571' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/AT-ISTA-20777 doi_confirm: '1' file: - access_level: open_access checksum: aae9d1ed53f7b67f75e289c26a02b72f content_type: application/pdf creator: pzivadin date_created: 2025-12-10T19:28:20Z date_updated: 2026-06-11T22:30:02Z embargo: 2026-06-11 file_id: '20778' file_name: 2025_Zivadinovic_Predrag_PhD_thesis.pdf file_size: 8105379 relation: main_file - access_level: closed checksum: 8a08a3804ce7d9d625fdf1631113da8c content_type: application/zip creator: pzivadin date_created: 2025-12-10T19:28:10Z date_updated: 2026-06-11T22:30:02Z embargo_to: open_access file_id: '20779' file_name: 2025_Zivadinovic_Predrag_PhD_thesis_source.zip file_size: 8512240 relation: source_file file_date_updated: 2026-06-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20777 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '104' project: - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Scale-free activity as a basis for spatial learning and memory in the brain type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- APC_amount: 7068 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19424' abstract: - lang: eng 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." acknowledged_ssus: - _id: M-Shop - _id: NanoFab 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." article_number: '3862' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Yona A full_name: Schell, Yona A id: fe39122d-06bb-11ec-a33b-9e22b40e40a5 last_name: Schell - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Maximilian full_name: Rimbach-Russ, Maximilian last_name: Rimbach-Russ - first_name: Stefano full_name: Bosco, Stefano last_name: Bosco - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Saez Mollejo J, Jirovec D, Schell YA, et al. Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. 2025;16. doi:10.1038/s41467-025-58969-y 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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-58969-y 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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-58969-y. ieee: J. Saez Mollejo et al., “Exchange anisotropies in microwave-driven singlet-triplet qubits,” Nature Communications, vol. 16. Springer Nature, 2025. 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. mla: Saez Mollejo, Jaime, et al. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” Nature Communications, vol. 16, 3862, Springer Nature, 2025, doi:10.1038/s41467-025-58969-y. 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). corr_author: '1' date_created: 2025-03-19T13:28:12Z date_published: 2025-04-24T00:00:00Z date_updated: 2026-11-04T23:30:52Z day: '24' ddc: - '530' department: - _id: GeKa doi: 10.1038/s41467-025-58969-y external_id: arxiv: - '2408.03224' isi: - '001475587400022' pmid: - '40274808' file: - access_level: open_access checksum: 13fe84cddc9d4e47213bf17acdac70d7 content_type: application/pdf creator: dernst date_created: 2025-05-05T07:08:23Z date_updated: 2025-05-05T07:08:23Z file_id: '19645' file_name: 2025_NatureComm_SaezMollejo.pdf file_size: 1548756 relation: main_file success: 1 file_date_updated: 2025-05-05T07:08:23Z fulldoi: https://doi.org/10.1038/s41467-025-58969-y has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _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 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: research_data url: https://ista.ac.at/en/news/the-shadow-of-an-electron/ record: - id: '19409' relation: research_data status: public - id: '19836' relation: dissertation_contains status: public scopus_import: '1' status: public title: Exchange anisotropies in microwave-driven singlet-triplet qubits tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher _id: '19836' 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" acknowledged_ssus: - _id: NanoFab - _id: M-Shop 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo citation: ama: 'Saez Mollejo J. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . 2025. doi:10.15479/AT-ISTA-19836' apa: 'Saez Mollejo, J. (2025). Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19836' chicago: 'Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19836.' ieee: 'J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.' ista: 'Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria.' mla: 'Saez Mollejo, Jaime. Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning . Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19836.' short: 'J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-06-13T09:01:50Z date_published: 2025-06-13T00:00:00Z date_updated: 2026-07-29T12:55:59Z day: '13' ddc: - '530' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/AT-ISTA-19836 doi_confirm: '1' file: - access_level: closed checksum: 643bfddead59857536cce4d57c775b32 content_type: application/x-zip-compressed creator: jsaezmol date_created: 2025-06-16T09:38:49Z date_updated: 2026-04-01T22:30:07Z embargo_to: open_access file_id: '19849' file_name: istaustriathesis-master - Copy.zip file_size: 59892829 relation: source_file - access_level: open_access checksum: e3dcb767fcc2b1787a455fdda991cefb content_type: application/pdf creator: jsaezmol date_created: 2025-06-18T08:50:16Z date_updated: 2026-04-01T22:30:07Z embargo: 2026-04-01 file_id: '19851' file_name: SaezMollejo_PhDFinal_pdfa-1b.pdf file_size: 22382376 relation: main_file file_date_updated: 2026-04-01T22:30:07Z fulldoi: https://doi.org/10.15479/AT-ISTA-19836 has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '175' project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19424' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: 'Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '19906' abstract: - lang: eng 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" acknowledged_ssus: - _id: M-Shop 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sarath S full_name: Suresh, Sarath S id: 3D126CC4-F248-11E8-B48F-1D18A9856A87 last_name: Suresh citation: ama: 'Suresh SS. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:10.15479/AT-ISTA-19906' apa: 'Suresh, S. S. (2025). Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19906' 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. https://doi.org/10.15479/AT-ISTA-19906.' 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.' 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.' mla: '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, doi:10.15479/AT-ISTA-19906.' 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.' corr_author: '1' date_created: 2025-06-26T08:39:08Z date_published: 2025-06-26T00:00:00Z date_updated: 2026-07-29T12:55:31Z day: '26' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/AT-ISTA-19906 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 302a07605a9e64ac247c2036d5f5b1cd content_type: application/pdf creator: cchlebak date_created: 2025-06-26T08:40:53Z date_updated: 2025-12-27T23:30:02Z embargo: 2025-12-27 file_id: '19907' file_name: Thesis_v9_PDFA2b.pdf file_size: 6504571 relation: main_file - access_level: closed checksum: 5d69d10bdacc24c27f02924379405bd9 content_type: application/x-zip-compressed creator: cchlebak date_created: 2025-06-26T08:41:24Z date_updated: 2025-12-27T23:30:02Z embargo_to: open_access file_id: '19908' file_name: Thesis Template - ISTA [istaustriathesis].zip file_size: 59092991 relation: source_file file_date_updated: 2025-12-27T23:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19906 has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '82' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10299' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: 'Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19386' abstract: - lang: eng text: "Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. " acknowledged_ssus: - _id: ScienComp 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). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:10.15479/AT-ISTA-19386 apa: Elkrewi, M. N. (2025). Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19386 chicago: Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19386. 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. mla: Elkrewi, Marwan N. Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19386. short: M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-11T12:54:31Z date_published: 2025-03-14T00:00:00Z date_updated: 2026-09-24T11:17:37Z day: '14' ddc: - '570' - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-19386 file: - access_level: closed checksum: 5549a8216c07e4c39281648912d72246 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: melkrewi date_created: 2025-03-26T07:06:56Z date_updated: 2026-03-26T23:30:03Z embargo_to: open_access file_id: '19462' file_name: Thesis_Marwan_Elkrewi.docx file_size: 25019680 relation: source_file - access_level: open_access checksum: aed2ba9965aa89b3414deae1ae9f4321 content_type: application/pdf creator: melkrewi date_created: 2025-03-26T07:06:22Z date_updated: 2026-03-26T23:30:03Z embargo: 2026-03-26 file_id: '19463' file_name: Thesis_Marwan_Elkrewi.pdf file_size: 17294844 relation: main_file file_date_updated: 2026-03-26T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19386 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '170' project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: eissn: - 2663-337X isbn: - '9783990780534' publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12248' relation: part_of_dissertation status: public - id: '10767' relation: part_of_dissertation status: public - id: '14613' relation: part_of_dissertation status: public - id: '10167' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public - id: '17890' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20449' abstract: - lang: eng 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. " acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett citation: ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449 apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449 chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449. ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025. ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449. short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-11T08:18:51Z date_published: 2025-10-10T00:00:00Z date_updated: 2026-09-24T11:11:01Z day: '10' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-20449 file: - access_level: open_access checksum: 26905c22bca417198a733d792d8ce422 content_type: application/pdf creator: vbett date_created: 2025-10-20T13:32:29Z date_updated: 2026-06-01T22:30:04Z embargo: 2026-06-01 file_id: '20507' file_name: 2025_Bett_Vincent_Thesis.pdf file_size: 18507283 relation: main_file - access_level: closed checksum: 6a09a8d126d3628bfd8a35202735f267 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vbett date_created: 2025-10-20T13:35:34Z date_updated: 2026-06-01T22:30:04Z embargo_to: open_access file_id: '20508' file_name: 2025_Bett_Vincent_Thesis.docx file_size: 17163921 relation: source_file file_date_updated: 2026-06-01T22:30:04Z fulldoi: https://doi.org/10.15479/AT-ISTA-20449 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '114' project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19735' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution and regulation of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19735' abstract: - lang: eng 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. acknowledged_ssus: - _id: ScienComp 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. article_number: msaf085 article_processing_charge: Yes article_type: original author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Minerva S full_name: Trejo Arellano, Minerva S id: 2b681148-eed5-11eb-b81b-ae229e8620f8 last_name: Trejo Arellano orcid: 0000-0002-1982-3475 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: 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. Molecular Biology and Evolution. 2025;42(5). doi:10.1093/molbev/msaf085 apa: Bett, V. K., Trejo Arellano, M. S., & 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. Oxford University Press. https://doi.org/10.1093/molbev/msaf085 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.” Molecular Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf085. 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,” Molecular Biology and Evolution, vol. 42, no. 5. Oxford University Press, 2025. 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. 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.” Molecular Biology and Evolution, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:10.1093/molbev/msaf085. short: V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025). corr_author: '1' date_created: 2025-05-25T22:16:56Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-11-04T23:31:05Z day: '01' ddc: - '570' department: - _id: BeVi - _id: DaZi doi: 10.1093/molbev/msaf085 external_id: isi: - '001483460200001' pmid: - '40202086' file: - access_level: open_access checksum: 6c14b03f94b4aadf8869be2c4366d077 content_type: application/pdf creator: dernst date_created: 2025-05-28T09:34:36Z date_updated: 2025-05-28T09:34:36Z file_id: '19756' file_name: 2025_MBE_Bett.pdf file_size: 1282772 relation: main_file success: 1 file_date_updated: 2025-05-28T09:34:36Z fulldoi: https://doi.org/10.1093/molbev/msaf085 has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git record: - id: '20449' relation: dissertation_contains status: public - id: '20444' relation: dissertation_contains status: deleted scopus_import: '1' status: public title: Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 42 year: '2025' ... --- OA_place: publisher _id: '20357' acknowledged_ssus: - _id: ScienComp - _id: E-Lib 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova citation: ama: Ruzickova N. Effect propagation in biological networks. 2025. doi:10.15479/AT-ISTA-20357 apa: Ruzickova, N. (2025). Effect propagation in biological networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20357 chicago: Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357. ieee: N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025. ista: Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria. mla: Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357. short: N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-15T17:04:48Z date_published: 2025-09-15T00:00:00Z date_updated: 2026-10-02T10:15:31Z day: '15' ddc: - '570' - '530' degree_awarded: PhD department: - _id: GradSch - _id: GaTk doi: 10.15479/AT-ISTA-20357 doi_confirm: '1' file: - access_level: closed checksum: 0582508d439b233497384f83a8307398 content_type: application/x-zip-compressed creator: cchlebak date_created: 2026-08-07T10:57:05Z date_updated: 2026-09-15T22:30:02Z embargo_to: open_access file_id: '22661' file_name: 2025_Ruzickova_Natalia_Thesis.zip file_size: 56464803 relation: source_file - access_level: open_access checksum: b722289fd550abede63adc27b9c61784 content_type: application/pdf creator: cchlebak date_created: 2026-08-07T10:57:34Z date_updated: 2026-09-15T22:30:02Z embargo: 2026-09-15 file_id: '22662' file_name: 2025_Ruzickova_Natalia_Thesis.pdf file_size: 30634378 relation: main_file file_date_updated: 2026-09-15T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20357 has_accepted_license: '1' keyword: - gene regulation - networks - omnigenic model - pancreas - collective behaviour language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '156' project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans publication_identifier: isbn: - 978-3-99078-066-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18525' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Effect propagation in biological networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20563' abstract: - lang: eng 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" acknowledgement: "The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:10.15479/AT-ISTA-20563 apa: Quattrocchi, F. (2025). Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20563 chicago: Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20563. ieee: F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025. ista: Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. mla: Quattrocchi, Filippo. Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20563. short: F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-28T13:10:49Z date_published: 2025-11-03T00:00:00Z date_updated: 2026-10-02T11:24:55Z day: '03' ddc: - '515' - '519' degree_awarded: PhD department: - _id: GradSch - _id: JaMa doi: 10.15479/AT-ISTA-20563 file: - access_level: open_access checksum: 6f55275bdf99992be3a6457d949dd664 content_type: application/pdf creator: fquattro date_created: 2025-11-17T21:04:15Z date_updated: 2026-01-01T23:30:03Z embargo: 2026-01-01 file_id: '20653' file_name: 2025_quattrocchi_filippo_thesis.pdf file_size: 4326411 relation: main_file - access_level: closed checksum: 707e580f5d993a214c0dba456b75837b content_type: application/zip creator: fquattro date_created: 2025-11-17T21:05:43Z date_updated: 2026-01-01T23:30:03Z embargo_to: open_access file_id: '20654' file_name: 2025_quattrocchi_thesis.zip file_size: 11726509 relation: source_file file_date_updated: 2026-01-01T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20563 has_accepted_license: '1' keyword: - optimal transport - kinetic equations - boundary value problems - quantization - gradient flows - homogenization language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '240' project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20569' relation: part_of_dissertation status: public - id: '20571' relation: part_of_dissertation status: public - id: '20570' relation: part_of_dissertation status: public - id: '18706' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository OA_type: green _id: '20569' 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.' 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." article_number: '2502.15665' article_processing_charge: No arxiv: 1 author: - first_name: Giovanni full_name: Brigati, Giovanni id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1 last_name: Brigati - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv. doi:10.48550/arXiv.2502.15665' apa: 'Brigati, G., Maas, J., & Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv. https://doi.org/10.48550/arXiv.2502.15665' chicago: 'Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2502.15665.' ieee: 'G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” arXiv. .' ista: 'Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. arXiv, 2502.15665.' mla: 'Brigati, Giovanni, et al. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” ArXiv, 2502.15665, doi:10.48550/arXiv.2502.15665.' short: G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:08Z date_published: 2025-08-10T00:00:00Z date_updated: 2026-11-04T23:31:11Z day: '10' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2502.15665 ec_funded: 1 external_id: arxiv: - '2502.15665' fulldoi: https://doi.org/10.48550/arXiv.2502.15665 keyword: - optimal transport - kinetic theory - second-order discrepancy - Vlasov equation - Wasserstein splines. language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2502.15665 month: '08' oa: 1 oa_version: Preprint project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: arXiv publication_status: draft related_material: record: - id: '20563' relation: dissertation_contains status: public status: public title: 'Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19533' abstract: - lang: eng 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" acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 citation: ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:10.15479/AT-ISTA-19533 apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533 chicago: Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533. ieee: R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025. ista: Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. mla: Sett, Riya. Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19533. short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-09T16:44:26Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-10-15T09:08:00Z day: '1' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-19533 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: ba6cd2289d0141a160a14fc97df1632f content_type: application/pdf creator: rsett date_created: 2025-04-10T11:33:22Z date_updated: 2025-10-11T22:30:02Z embargo: 2025-10-11 file_id: '19538' file_name: PhD_Thesis_Riya_Sett_pdfa.pdf file_size: 4129208 relation: main_file - access_level: closed checksum: ee63a94cb8f7adf5e766903028b81ed6 content_type: application/x-zip-compressed creator: rsett date_created: 2025-04-10T11:34:08Z date_updated: 2025-10-11T22:30:02Z embargo_to: open_access file_id: '19539' file_name: PhD Thesis Riya Sett.zip file_size: 6646110 relation: source_file file_date_updated: 2025-10-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19533 has_accepted_license: '1' 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 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '109' project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18978' relation: research_data status: public - id: '19280' relation: part_of_dissertation status: public - id: '13117' relation: part_of_dissertation status: public - id: '17183' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Quantum remote sensing and non-equilibrium phase transitions in the microwave regime tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19280' 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. acknowledged_ssus: - _id: M-Shop - _id: NanoFab 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.' article_number: '063601' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: M. full_name: Zens, M. last_name: Zens - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka orcid: 0009-0005-0878-3032 - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Przemyslaw D full_name: Zielinski, Przemyslaw D id: e198fcc4-f6e0-11ea-865d-b6a256760ee8 last_name: Zielinski - first_name: H. S. full_name: Dhar, H. S. last_name: Dhar - first_name: D. O. full_name: Krimer, D. O. last_name: Krimer - first_name: S. full_name: Rotter, S. last_name: Rotter - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Zens M, Zemlicka M, et al. Observation of collapse and revival in a superconducting atomic frequency comb. Physical Review Letters. 2025;134(6). doi:10.1103/PhysRevLett.134.063601 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. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.063601 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.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.063601. ieee: E. Redchenko et al., “Observation of collapse and revival in a superconducting atomic frequency comb,” Physical Review Letters, vol. 134, no. 6. American Physical Society, 2025. 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. mla: Redchenko, Elena, et al. “Observation of Collapse and Revival in a Superconducting Atomic Frequency Comb.” Physical Review Letters, vol. 134, no. 6, 063601, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.063601. 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). corr_author: '1' date_created: 2025-03-02T23:01:52Z date_published: 2025-02-14T00:00:00Z date_updated: 2026-11-04T23:31:12Z day: '14' ddc: - '530' department: - _id: JoFi doi: 10.1103/PhysRevLett.134.063601 ec_funded: 1 external_id: arxiv: - '2310.04200' isi: - '001454696700003' pmid: - '40021171' file: - access_level: open_access checksum: 633d6c5ddd9b805da22c5839d3d48df6 content_type: application/pdf creator: dernst date_created: 2025-03-04T10:40:50Z date_updated: 2025-03-04T10:40:50Z file_id: '19291' file_name: 2025_PhysReviewLetters_Redchenko.pdf file_size: 2080408 relation: main_file success: 1 file_date_updated: 2025-03-04T10:40:50Z fulldoi: https://doi.org/10.1103/PhysRevLett.134.063601 has_accepted_license: '1' intvolume: ' 134' isi: 1 issue: '6' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 26B354CA-B435-11E9-9278-68D0E5697425 name: Controllable Collective States of Superconducting Qubit Ensembles publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '19533' relation: dissertation_contains status: public scopus_import: '1' status: public title: Observation of collapse and revival in a superconducting atomic frequency comb tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 134 year: '2025' ... --- OA_place: publisher _id: '20212' abstract: - lang: eng 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. " acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 citation: ama: Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:10.15479/AT-ISTA-20212 apa: Miranda, O. (2025). Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20212 chicago: Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20212. ieee: O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025. ista: Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. mla: Miranda, Osvaldo. Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20212. short: O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-22T14:07:00Z date_published: 2025-08-22T00:00:00Z date_updated: 2026-10-02T12:16:56Z day: '22' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/AT-ISTA-20212 doi_confirm: '1' file: - access_level: closed checksum: 3331f76bbef74ff4908e2d2c9262045c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: omiranda date_created: 2025-08-26T09:03:50Z date_updated: 2026-08-26T22:30:02Z embargo_to: open_access file_id: '20230' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.docx file_size: 32887334 relation: source_file - access_level: open_access checksum: 02509d50cff8e35c5bcbf71e8d658176 content_type: application/pdf creator: omiranda date_created: 2025-08-26T09:05:55Z date_updated: 2026-08-26T22:30:02Z embargo: 2026-08-26 file_id: '20231' file_name: 2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf file_size: 28636240 relation: main_file file_date_updated: 2026-08-26T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20212 has_accepted_license: '1' keyword: - Pten - mtor - cortical development - MADM - Mapk language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '119' project: - _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d grant_number: '26253' name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development publication_identifier: isbn: - 978-3-99078-063-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17425' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Unraveling the role of Pten in cortical stem cell lineage progression using MADM type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20117' 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. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Yiqun full_name: Wang, Yiqun id: 82F537F2-B517-11E9-84D7-6433E6697425 last_name: Wang citation: ama: Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117 apa: Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20117 chicago: Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20117. ieee: Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025. ista: Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. mla: Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20117. short: Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-04T15:24:21Z date_published: 2025-08-04T00:00:00Z date_updated: 2026-10-02T12:33:36Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-20117 doi_confirm: '1' file: - access_level: closed checksum: 36b87c17d12c7bf5955d6d812acb8d77 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: yiqwang date_created: 2025-08-22T08:22:10Z date_updated: 2026-09-03T22:30:03Z embargo_to: open_access file_id: '20209' file_name: 2025_Wang_Yiqun_Thesis.docx file_size: 25798848 relation: source_file - access_level: open_access checksum: 8d7a2383f66377da675d379ec30ea0fe content_type: application/pdf creator: yiqwang date_created: 2025-08-22T10:32:30Z date_updated: 2026-09-03T22:30:03Z embargo: 2026-09-03 file_id: '20211' file_name: 2025_Wang_Yiqun_Thesis.pdf file_size: 12628313 relation: main_file file_date_updated: 2026-09-03T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20117 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '108' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18063' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: The role of dynamin related protein 2A in cytokinin regulated plant growth and development type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20187' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: LifeSc 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)." article_number: e70396 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Frédérique full_name: Tellier, Frédérique last_name: Tellier - first_name: Adrijana full_name: Smoljan, Adrijana id: cced8a85-223e-11ed-af04-b0596c55053b last_name: Smoljan - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Petr full_name: Valošek, Petr id: 3CDB6F94-F248-11E8-B48F-1D18A9856A87 last_name: Valošek - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jean Denis full_name: Faure, Jean Denis last_name: Faure - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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. Plant Journal. 2025;123(3). doi:10.1111/tpj.70396 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. Plant Journal. Wiley. https://doi.org/10.1111/tpj.70396 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.” Plant Journal. Wiley, 2025. https://doi.org/10.1111/tpj.70396. ieee: D. Babic et al., “Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development,” Plant Journal, vol. 123, no. 3. Wiley, 2025. 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. mla: Babic, David, et al. “Biosynthesis of Very Long-Chain Fatty Acids Is Required for Arabidopsis Auxin-Mediated Embryonic and Post-Embryonic Development.” Plant Journal, vol. 123, no. 3, e70396, Wiley, 2025, doi:10.1111/tpj.70396. 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). corr_author: '1' date_created: 2025-08-17T22:01:36Z date_published: 2025-08-01T00:00:00Z date_updated: 2026-11-04T23:31:15Z day: '01' ddc: - '580' department: - _id: EvBe - _id: JiFr - _id: GradSch doi: 10.1111/tpj.70396 external_id: isi: - '001547884300001' pmid: - '40782342' file: - access_level: open_access checksum: 1cdc3341d2d23101abca72521f1f23cb content_type: application/pdf creator: dernst date_created: 2025-09-01T14:09:31Z date_updated: 2025-09-01T14:09:31Z file_id: '20264' file_name: 2025_PlantJournal_Babic.pdf file_size: 5791111 relation: main_file success: 1 file_date_updated: 2025-09-01T14:09:31Z fulldoi: https://doi.org/10.1111/tpj.70396 has_accepted_license: '1' intvolume: ' 123' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis publication: Plant Journal publication_identifier: eissn: - 1365-313X issn: - 0960-7412 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '20362' relation: dissertation_contains status: public scopus_import: '1' status: public title: Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2025' ... --- OA_place: publisher _id: '20362' abstract: - lang: eng 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." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic citation: ama: Babic D. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. 2025. doi:10.15479/AT-ISTA-20362 apa: Babic, D. (2025). Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20362 chicago: Babic, David. “Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20362. ieee: D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025. ista: Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria. mla: Babic, David. Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20362. short: D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-17T13:28:01Z date_published: 2025-09-18T00:00:00Z date_updated: 2026-10-16T07:59:32Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 10.15479/AT-ISTA-20362 doi_confirm: '1' file: - access_level: open_access checksum: 5ecf274281a54a41e0288bc79edf7492 content_type: application/pdf creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo: 2026-09-25 file_id: '20388' file_name: 2025_David_Babic_Thesis.pdf file_size: 7501548 relation: main_file - access_level: closed checksum: 2703e548390de0a1af7a707137e8ab3b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dbabic date_created: 2025-09-24T13:43:14Z date_updated: 2026-09-25T22:30:02Z embargo_to: open_access file_id: '20389' file_name: Thesis_Babic_draft.docx file_size: 23206052 relation: source_file file_date_updated: 2026-09-25T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20362 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '116' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository _id: '21427' 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. acknowledgement: "European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360" article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Erik full_name: Sahai, Erik last_name: Sahai - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. doi:10.1101/2025.05.20.655037 apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., & Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv. https://doi.org/10.1101/2025.05.20.655037 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.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.20.655037. ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” bioRxiv. . 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, 10.1101/2025.05.20.655037. mla: Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” BioRxiv, doi:10.1101/2025.05.20.655037. short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-03-11T08:40:06Z date_published: 2025-09-25T00:00:00Z date_updated: 2026-11-04T23:31:15Z day: '25' ddc: - '539' - '570' department: - _id: GradSch - _id: EdHa - _id: MiSi - _id: NanoFab - _id: AnSa doi: 10.1101/2025.05.20.655037 fulldoi: https://doi.org/10.1101/2025.05.20.655037 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.20.655037 month: '09' oa: 1 oa_version: Preprint project: - _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd grant_number: '101071793' name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces' - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication: bioRxiv publication_status: draft related_material: record: - id: '21439' relation: research_data status: public - id: '22963' relation: later_version status: public - id: '21423' relation: dissertation_contains status: public status: public title: Substrate heterogeneity promotes cancer cell dissemination through interface roughening tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ...