[{"file_date_updated":"2026-02-01T23:30:02Z","date_updated":"2026-04-07T12:40:42Z","day":"04","year":"2025","publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation","date_published":"2025-03-04T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"has_accepted_license":"1","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula","citation":{"ieee":"C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula,” Institute of Science and Technology Austria, 2025.","ama":"Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19271\">10.15479/AT-ISTA-19271</a>","chicago":"Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19271\">https://doi.org/10.15479/AT-ISTA-19271</a>.","apa":"Önal, C. (2025). <i>Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19271\">https://doi.org/10.15479/AT-ISTA-19271</a>","short":"C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025.","ista":"Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria.","mla":"Önal, Cihan. <i>Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19271\">10.15479/AT-ISTA-19271</a>."},"project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"_id":"19271","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"OA_place":"publisher","date_created":"2025-02-28T14:15:53Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"abstract":[{"text":"The medial habenula (MHb) is implicated in regulating emotional responses\r\nto aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses. However, there is little evidence for structural or\r\nfunctional lateralization in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties of the left and right MHb\r\nafferents to the IPN in mice and addressed whether these synaptic connections\r\nselectively influence the expression of conditioned fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs from both left and right MHb.\r\nElectrophysiological recordings from the same postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses exhibit lower release\r\nprobability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings suggest that\r\nlateralized pathways could represent a fundamental principle in the neural\r\nregulation of emotion across species.","lang":"eng"}],"acknowledgement":"I would like to thank the European Research Council and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association for providing financial support and opportunities, which were important in allowing me to present my work. I also wish to thank the\r\nPreclinical Facility, especially Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani, and Thomas Menner, whose technical expertise often saved the day.","month":"03","oa":1,"status":"public","corr_author":"1","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"}],"ddc":["570","571","573","599"],"file":[{"checksum":"c1a4d75a7471de9f954697b06cd18d28","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25869143,"file_id":"19272","relation":"source_file","access_level":"closed","date_created":"2025-02-28T13:57:01Z","date_updated":"2026-02-01T23:30:02Z","embargo_to":"open_access","creator":"hoenal","file_name":"Cihan_Onal_Thesis_Final.docx"},{"content_type":"application/pdf","file_size":12077596,"file_id":"19273","relation":"main_file","access_level":"open_access","embargo":"2026-02-01","checksum":"de4e62147ab9f04098dc8cd898c630da","creator":"hoenal","file_name":"Cihan_Onal_Thesis_Final_pdfa.pdf","date_created":"2025-02-28T13:57:04Z","date_updated":"2026-02-01T23:30:02Z"}],"author":[{"first_name":"Hüseyin C","id":"4659D740-F248-11E8-B48F-1D18A9856A87","last_name":"Önal","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C"}],"doi":"10.15479/AT-ISTA-19271","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9437"},{"relation":"part_of_dissertation","status":"public","id":"15084"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"oa_version":"Published Version","author":[{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","full_name":"Hlavata, Annamaria","last_name":"Hlavata"}],"file":[{"file_id":"19448","file_size":23506747,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","embargo_to":"open_access","date_updated":"2026-03-20T23:30:04Z","date_created":"2025-03-24T12:48:36Z","file_name":"PhD_Thesis_Hlavata_final_submission.docx","creator":"ahlavata"},{"checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","embargo":"2026-03-20","relation":"main_file","access_level":"open_access","file_id":"19449","content_type":"application/pdf","file_size":9478591,"date_updated":"2026-03-20T23:30:04Z","date_created":"2025-03-24T12:51:10Z","creator":"ahlavata","file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf"}],"doi":"10.15479/10.15479/AT-ISTA-19431","alternative_title":["ISTA Thesis"],"publication_status":"published","title":"Regulation of Cytoplasmic RNA Polymerase II","citation":{"ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025.","chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>."},"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2025-03-20T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"has_accepted_license":"1","file_date_updated":"2026-03-20T23:30:04Z","date_updated":"2026-04-07T11:46:32Z","day":"20","publication_identifier":{"isbn":["978-3-99078-055-8"],"eissn":["2663-337X"]},"type":"dissertation","year":"2025","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"ddc":["572"],"month":"03","oa":1,"status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"}],"abstract":[{"text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm.","lang":"eng"}],"acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","_id":"19431","OA_place":"publisher","page":"83","date_created":"2025-03-20T12:52:47Z","degree_awarded":"PhD"},{"ddc":["577"],"acknowledged_ssus":[{"_id":"LifeSc"}],"corr_author":"1","status":"public","oa":1,"month":"02","abstract":[{"text":"Social interaction networks of insect colonies facilitate efficient information exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission. While circadian rhythms\r\ninfluence individual behaviour, their role in shaping colony-level defences against pathogens\r\nremains unexplored. Here, we investigate whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies are exposed to a pathogen during the day or the night.\r\nWe first establish baseline daily variations in activity and network dynamics in pathogen-free\r\ncolonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting of nurses and the queen. These findings underscore the robustness and adaptability\r\nof ant colonies in balancing circadian rhythms with effective social immune responses.","lang":"eng"}],"acknowledgement":"Thank you to the Lab Support Facility at ISTA. Thank you to the European Research Council (ERC) for their funding under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402, to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt).","ec_funded":1,"supervisor":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_created":"2025-03-06T12:16:54Z","page":"85","_id":"19302","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025.","mla":"Sartoris, Linda. <i>The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>.","ista":"Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria.","ieee":"L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025.","chicago":"Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>.","ama":"Sartoris L. The effect of circadian rhythm on organisational immunity of ant colonies. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19302\">10.15479/AT-ISTA-19302</a>","apa":"Sartoris, L. (2025). <i>The effect of circadian rhythm on organisational immunity of ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19302\">https://doi.org/10.15479/AT-ISTA-19302</a>"},"title":"The effect of circadian rhythm on organisational immunity of ant colonies","OA_type":"closed access","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"date_published":"2025-02-24T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"type":"dissertation","year":"2025","day":"24","date_updated":"2026-03-02T23:31:14Z","file_date_updated":"2026-03-02T23:31:13Z","publication_status":"published","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19302","author":[{"id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","first_name":"Linda","full_name":"Sartoris, Linda","last_name":"Sartoris"}],"file":[{"file_name":"Thesis_Linda_Sartoris.docx","creator":"lsartori","date_created":"2025-03-07T10:16:11Z","date_updated":"2026-02-23T23:30:03Z","embargo_to":"open_access","checksum":"7e9466dcf3681454211b74b5107e9f7b","relation":"source_file","access_level":"closed","file_size":7129583,"file_id":"19310","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2025-03-11T10:42:20Z","date_updated":"2026-03-02T23:31:13Z","embargo_to":"open_access","creator":"lsartori","file_name":"thesis_Sartoris_for_print.pdf","checksum":"2ccfcf32f0590bb0ec1a488e606a73f5","file_id":"19384","content_type":"application/pdf","file_size":3199703,"relation":"other","access_level":"closed","description":"for printing purposes only"},{"creator":"lsartori","file_name":"Thesis_Linda_Sartoris.pdf","date_created":"2025-03-11T10:52:00Z","date_updated":"2026-02-23T23:30:03Z","checksum":"1d1f3c1279065b1a7f407ff6d1ee1503","embargo":"2026-02-23","access_level":"open_access","relation":"main_file","file_id":"19385","file_size":3183186,"content_type":"application/pdf"}]},{"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19456","author":[{"first_name":"Andrea D","id":"3F158B32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1727-6612","last_name":"Cumpelik","full_name":"Cumpelik, Andrea D"}],"file":[{"file_id":"19457","file_size":11869040,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2025-09-30","checksum":"1c7573303d8e5f6da3eb03d59055390f","date_updated":"2025-09-30T22:30:02Z","date_created":"2025-03-25T11:07:55Z","creator":"acumpeli","file_name":"2025_Thesis_Cumpelik_corrections_PDFA.pdf"},{"checksum":"b93265ebd9a53f7a14100d0d48b4ff5b","relation":"source_file","access_level":"closed","file_size":20436467,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19458","creator":"acumpeli","file_name":"2025_Thesis_Cumpelik_corrections.docx","date_created":"2025-03-25T11:08:05Z","date_updated":"2025-09-30T22:30:02Z","embargo_to":"open_access"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"OA_embargo":"6 months","citation":{"ama":"Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>","ieee":"A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025.","chicago":"Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>.","apa":"Cumpelik, A. D. (2025). <i>The role of prefrontal spatial coding in supporting a contextual association task</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>","short":"A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025.","mla":"Cumpelik, Andrea D. <i>The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>.","ista":"Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria."},"title":"The role of prefrontal spatial coding in supporting a contextual association task","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"date_published":"2025-02-18T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-056-5"],"issn":["2663-337X"]},"year":"2025","type":"dissertation","day":"18","date_updated":"2026-04-07T12:37:58Z","file_date_updated":"2025-09-30T22:30:02Z","ddc":["612"],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"corr_author":"1","status":"public","oa":1,"month":"02","abstract":[{"lang":"eng","text":"Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. "}],"supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"}],"publisher":"Institute of Science and Technology Austria","keyword":["neuroscience","decision making","learning","cognitive flexibility","medial prefrontal cortex","hippocampus","electrophysiology"],"degree_awarded":"PhD","page":"96","date_created":"2025-03-25T11:22:38Z","OA_place":"publisher","_id":"19456"},{"degree_awarded":"PhD","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"19763","OA_place":"publisher","date_created":"2025-05-30T09:14:58Z","page":"129","abstract":[{"lang":"eng","text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation."}],"acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","month":"05","oa":1,"status":"public","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","file_date_updated":"2025-11-30T23:30:02Z","day":"29","date_updated":"2026-04-14T09:50:53Z","has_accepted_license":"1","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"date_published":"2025-05-29T00:00:00Z","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","project":[{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","citation":{"ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>.","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>.","short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025."},"alternative_title":["ISTA Thesis"],"publication_status":"published","doi":"10.15479/AT-ISTA-19763","author":[{"first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093","last_name":"Rus","full_name":"Rus, Stefanie"}],"file":[{"relation":"main_file","access_level":"open_access","file_size":42879974,"file_id":"19764","content_type":"application/pdf","checksum":"8cd7fe3ca990adbcafdece119aa0973d","embargo":"2025-11-30","file_name":"Thesis_Lehr_PDFA.pdf","creator":"cchlebak","date_updated":"2025-11-30T23:30:02Z","date_created":"2025-05-30T09:10:22Z"},{"file_name":"Thesis_Lehr_emptyPages.docx","creator":"cchlebak","date_created":"2025-05-30T09:31:15Z","date_updated":"2025-11-30T23:30:02Z","embargo_to":"open_access","checksum":"0c87dd5fc803450a47b20736b5f86a2f","relation":"source_file","access_level":"closed","file_size":18731094,"file_id":"19765","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18601"},{"id":"17148","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"18807"},{"status":"public","relation":"part_of_dissertation","id":"13136"}]}},{"doi":"10.1016/j.devcel.2024.10.024","author":[{"full_name":"Rus, Stefanie","last_name":"Rus","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","full_name":"Minchington, Thomas"},{"first_name":"Martina","id":"48A59534-F248-11E8-B48F-1D18A9856A87","last_name":"Greunz","full_name":"Greunz, Martina"},{"full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"dernst","file_name":"2025_DevelopmentalCell_Lehr.pdf","date_created":"2025-04-16T10:54:07Z","date_updated":"2025-04-16T10:54:07Z","success":1,"access_level":"open_access","relation":"main_file","file_size":6994499,"file_id":"19584","content_type":"application/pdf","checksum":"bb58db4a908a1f4aabe4004706154541"}],"oa_version":"Published Version","external_id":{"isi":["001434279000001"],"pmid":["39603235"]},"pmid":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"publication_status":"published","issue":"4","intvolume":"        60","type":"journal_article","year":"2025","publication_identifier":{"issn":["1534-5807"]},"date_updated":"2026-09-05T22:30:38Z","day":"24","file_date_updated":"2025-04-16T10:54:07Z","has_accepted_license":"1","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"date_published":"2025-02-24T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","volume":60,"project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"citation":{"ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Elsevier, pp. 567–580, 2025.","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>"},"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","scopus_import":"1","page":"567-580","date_created":"2025-01-09T11:25:47Z","OA_place":"publisher","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"18807","abstract":[{"text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.","lang":"eng"}],"acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","article_type":"original","publisher":"Elsevier","isi":1,"corr_author":"1","oa":1,"status":"public","month":"02","publication":"Developmental Cell","ddc":["570"],"quality_controlled":"1"},{"alternative_title":["ISTA Thesis"],"publication_status":"published","oa_version":"Published Version","author":[{"first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","orcid":"0009-0002-5890-120X","last_name":"Inumella","full_name":"Inumella, Syamala"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"19757","file_size":8292363,"embargo":"2026-05-23","checksum":"847ec70b2e40f50e0ddc7b8da201d52c","date_updated":"2026-05-23T22:30:02Z","date_created":"2025-05-28T11:59:11Z","creator":"sinumell","file_name":"Final Thesis_Syamala Inumella.pdf"},{"checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","access_level":"closed","relation":"source_file","file_size":7145703,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"19758","date_updated":"2026-05-23T22:30:02Z","date_created":"2025-05-28T11:59:11Z","embargo_to":"open_access","file_name":"Final Thesis_Syamala Inumella.docx","creator":"sinumell"}],"doi":"10.15479/AT-ISTA-19722","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["580"],"month":"05","oa":1,"status":"public","corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"acknowledgement":"Special thanks to the Plant Facility.","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."}],"OA_place":"publisher","_id":"19722","page":"113","date_created":"2025-05-23T15:21:29Z","degree_awarded":"PhD","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","citation":{"short":"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. <i>Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19722\">10.15479/AT-ISTA-19722</a>","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>.","apa":"Inumella, S. (2025). <i>Molecular mechanisms of microtubule reorganization in elongating root epidermal cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19722\">https://doi.org/10.15479/AT-ISTA-19722</a>"},"OA_embargo":"12","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_published":"2025-05-23T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"has_accepted_license":"1","file_date_updated":"2026-05-23T22:30:02Z","date_updated":"2026-06-12T08:34:29Z","day":"23","year":"2025","publication_identifier":{"isbn":["978-3-99078-059-6"],"issn":["2663-337X"]},"type":"dissertation"},{"related_material":{"record":[{"id":"19735","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15009"}]},"oa_version":"Published Version","file":[{"file_name":"2025_Bett_Vincent_Thesis.pdf","creator":"vbett","date_updated":"2026-06-01T22:30:04Z","date_created":"2025-10-20T13:32:29Z","access_level":"open_access","relation":"main_file","file_id":"20507","file_size":18507283,"content_type":"application/pdf","checksum":"26905c22bca417198a733d792d8ce422","embargo":"2026-06-01"},{"checksum":"6a09a8d126d3628bfd8a35202735f267","file_id":"20508","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":17163921,"access_level":"closed","relation":"source_file","date_created":"2025-10-20T13:35:34Z","date_updated":"2026-06-01T22:30:04Z","embargo_to":"open_access","file_name":"2025_Bett_Vincent_Thesis.docx","creator":"vbett"}],"author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","full_name":"Bett, Vincent K"}],"doi":"10.15479/AT-ISTA-20449","alternative_title":["ISTA Thesis"],"publication_status":"published","title":"Evolution and regulation of the Z chromosome","citation":{"ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","chicago":"Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>.","apa":"Bett, V. K. (2025). <i>Evolution and regulation of the Z chromosome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>","ama":"Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>"},"project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2025-10-10T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file_date_updated":"2026-06-01T22:30:04Z","date_updated":"2026-06-12T08:32:16Z","day":"10","year":"2025","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["576"],"month":"10","status":"public","oa":1,"corr_author":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","abstract":[{"text":"Males and females of many  species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria  ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. ","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"20449","OA_place":"publisher","date_created":"2025-10-11T08:18:51Z","page":"114","degree_awarded":"PhD"},{"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_published":"2025-11-25T00:00:00Z","language":[{"iso":"eng"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","date_updated":"2026-04-28T13:20:36Z","day":"25","file_date_updated":"2026-03-01T23:30:03Z","project":[{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"},{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"citation":{"ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>","apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria."},"title":"Using genealogies to study the genomic basis of species divergence","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us."}],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"268","date_created":"2025-11-25T13:19:11Z","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"20694","OA_place":"publisher","ddc":["576","578"],"acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","oa":1,"status":"public","month":"11","oa_version":"Published Version","doi":"10.15479/AT-ISTA-20694","file":[{"date_updated":"2026-03-01T23:30:03Z","date_created":"2025-12-01T13:53:36Z","creator":"apal","file_name":"2025_Pal_Arka_Thesis.pdf","access_level":"open_access","relation":"main_file","file_size":42723135,"content_type":"application/pdf","file_id":"20721","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","embargo":"2026-03-01"},{"checksum":"166d832b08d0434ce407f8f3cb930fe5","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20722","file_size":60632116,"relation":"source_file","access_level":"closed","file_name":"2025_Pal_Arka_Thesis.docx","creator":"apal","date_created":"2025-12-01T13:53:39Z","date_updated":"2026-03-01T23:30:03Z","embargo_to":"open_access"}],"author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","last_name":"Pal"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12159"},{"id":"14796","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"20190"}]},"publication_status":"published","alternative_title":["ISTA Thesis"]},{"external_id":{"isi":["001546622100001"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20694"}],"link":[{"url":"https://ista.ac.at/en/news/snapdragon-secrets/","relation":"press_release","description":"News on ISTA website"}]},"author":[{"first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","full_name":"Shipilina, Daria","last_name":"Shipilina","orcid":"0000-0002-1145-9226"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"first_name":"Adrian J.","last_name":"Mcnairn","full_name":"Mcnairn, Adrian J."},{"full_name":"Grenier, Jennifer K.","last_name":"Grenier","first_name":"Jennifer K."},{"last_name":"Kucka","full_name":"Kucka, Marek","first_name":"Marek"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"file":[{"checksum":"c586fc674df4e7dd6e43aef87a52c6f6","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":9886694,"file_id":"20958","success":1,"date_updated":"2026-01-05T13:47:47Z","date_created":"2026-01-05T13:47:47Z","file_name":"2025_MolecEcology_Pal.pdf","creator":"dernst"}],"doi":"10.1111/mec.70067","oa_version":"Published Version","PlanS_conform":"1","article_number":"e70067","publication_status":"published","issue":"22","intvolume":"        34","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>, vol. 34, no. 22, e70067, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>.","short":"A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).","ama":"Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. 2025;34(22). doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>","ieee":"A. Pal <i>et al.</i>, “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” <i>Molecular Ecology</i>, vol. 34, no. 22. Wiley, 2025.","apa":"Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>","chicago":"Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>."},"title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","volume":34,"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"date_updated":"2026-09-05T22:30:42Z","day":"01","file_date_updated":"2026-01-05T13:47:47Z","type":"journal_article","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"year":"2025","language":[{"iso":"eng"}],"date_published":"2025-11-01T00:00:00Z","has_accepted_license":"1","department":[{"_id":"NiBa"}],"status":"public","oa":1,"publication":"Molecular Ecology","month":"11","isi":1,"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"quality_controlled":"1","date_created":"2025-08-17T22:01:37Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"20190","OA_place":"publisher","publisher":"Wiley","article_type":"original","abstract":[{"lang":"eng","text":"A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression."}],"acknowledgement":"We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. "},{"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>.","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria.","mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025."},"title":"Social immunity in a tri-partite host-pathogen relationship","date_updated":"2026-04-07T12:39:58Z","day":"11","file_date_updated":"2026-01-15T23:30:03Z","year":"2025","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2025-07-11T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"has_accepted_license":"1","oa":1,"status":"public","month":"07","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"ddc":["570"],"date_created":"2025-07-10T14:12:20Z","page":"138","_id":"19993","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"OA_place":"publisher","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","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."}],"file":[{"file_name":"Thesis_Florian_Strahodinsky_DOCX.docx","creator":"fstrahod","embargo_to":"open_access","date_created":"2025-07-14T13:18:37Z","date_updated":"2026-01-15T23:30:03Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20021","file_size":9857392,"checksum":"df3a02f0d937ea9a3d79d5fb94fff097"},{"embargo":"2026-01-15","checksum":"7164c21fe1946e839f7b8acd255ce803","access_level":"open_access","relation":"main_file","file_id":"20022","file_size":6439602,"content_type":"application/pdf","date_updated":"2026-01-15T23:30:03Z","date_created":"2025-07-14T13:18:38Z","creator":"fstrahod","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf"}],"author":[{"id":"979E35EE-C996-11E9-8C7C-CF13E6697425","first_name":"Florian","full_name":"Strahodinsky, Florian","last_name":"Strahodinsky"}],"doi":"10.15479/AT-ISTA-19993","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"]},{"publication_status":"published","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT-ISTA-20470","author":[{"full_name":"Wu, Bryan","last_name":"Wu","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","first_name":"Bryan"}],"file":[{"checksum":"d32ea83f259f6b0506325cd57b1d44c3","file_size":10603235,"file_id":"20516","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"brwu","file_name":"2025_Wu_Bryan_Thesis.docx","date_created":"2025-10-21T17:33:27Z","date_updated":"2026-04-30T22:30:02Z","embargo_to":"open_access"},{"file_name":"2025_Wu_Bryan_Thesis.pdf","creator":"brwu","date_updated":"2026-04-30T22:30:02Z","date_created":"2025-10-21T17:33:26Z","relation":"main_file","access_level":"open_access","file_id":"20517","content_type":"application/pdf","file_size":6251936,"embargo":"2026-04-30","checksum":"53590046fd3244c5550b4022282449d2"}],"oa_version":"Published Version","degree_awarded":"PhD","date_created":"2025-10-15T13:30:21Z","page":"102","_id":"20470","OA_place":"publisher","abstract":[{"text":"Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems.","lang":"eng"}],"supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","oa":1,"status":"public","month":"10","ddc":["579"],"type":"dissertation","year":"2025","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-05-06T08:01:28Z","day":"30","file_date_updated":"2026-04-30T22:30:02Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"date_published":"2025-10-30T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","citation":{"short":"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. <i>An Examination on Phages as a Naturally Composable System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>.","apa":"Wu, B. (2025). <i>An examination on phages as a naturally composable system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","ama":"Wu B. An examination on phages as a naturally composable system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>","chicago":"Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>."},"title":"An examination on phages as a naturally composable system"},{"intvolume":"        42","article_number":"msaf085","publication_status":"published","issue":"5","oa_version":"Published Version","author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","full_name":"Bett, Vincent K"},{"id":"2b681148-eed5-11eb-b81b-ae229e8620f8","first_name":"Minerva S","full_name":"Trejo Arellano, Minerva S","orcid":"0000-0002-1982-3475","last_name":"Trejo Arellano"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"6c14b03f94b4aadf8869be2c4366d077","relation":"main_file","access_level":"open_access","file_size":1282772,"content_type":"application/pdf","file_id":"19756","date_created":"2025-05-28T09:34:36Z","date_updated":"2025-05-28T09:34:36Z","success":1,"file_name":"2025_MBE_Bett.pdf","creator":"dernst"}],"doi":"10.1093/molbev/msaf085","related_material":{"record":[{"id":"20449","status":"public","relation":"dissertation_contains"},{"status":"deleted","relation":"dissertation_contains","id":"20444"}],"link":[{"url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git","relation":"software"}]},"pmid":1,"DOAJ_listed":"1","external_id":{"isi":["001483460200001"],"pmid":["40202086"]},"publisher":"Oxford University Press","abstract":[{"text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.","lang":"eng"}],"article_type":"original","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.","scopus_import":"1","date_created":"2025-05-25T22:16:56Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"19735","OA_place":"publisher","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","ddc":["570"],"status":"public","oa":1,"publication":"Molecular Biology and Evolution","month":"05","isi":1,"corr_author":"1","language":[{"iso":"eng"}],"date_published":"2025-05-01T00:00:00Z","has_accepted_license":"1","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"day":"01","date_updated":"2026-09-05T22:30:44Z","file_date_updated":"2025-05-28T09:34:36Z","type":"journal_article","year":"2025","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"citation":{"mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>"},"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","volume":42,"project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development"},{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"article_processing_charge":"Yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"gold"},{"doi_confirm":"1","author":[{"first_name":"Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425","last_name":"Zivadinovic","full_name":"Zivadinovic, Predrag"}],"file":[{"embargo":"2026-06-11","checksum":"aae9d1ed53f7b67f75e289c26a02b72f","file_id":"20778","content_type":"application/pdf","file_size":8105379,"relation":"main_file","access_level":"open_access","date_updated":"2026-06-11T22:30:02Z","date_created":"2025-12-10T19:28:20Z","creator":"pzivadin","file_name":"2025_Zivadinovic_Predrag_PhD_thesis.pdf"},{"access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"20779","file_size":8512240,"checksum":"8a08a3804ce7d9d625fdf1631113da8c","file_name":"2025_Zivadinovic_Predrag_PhD_thesis_source.zip","creator":"pzivadin","embargo_to":"open_access","date_updated":"2026-06-11T22:30:02Z","date_created":"2025-12-10T19:28:10Z"}],"doi":"10.15479/AT-ISTA-20777","oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"das_tickbox":"1","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025.","mla":"Zivadinovic, Predrag. <i>Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>.","ista":"Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria.","ama":"Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20777\">10.15479/AT-ISTA-20777</a>","chicago":"Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>.","ieee":"P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025.","apa":"Zivadinovic, P. (2025). <i>Scale-free activity as a basis for spatial learning and memory in the brain</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20777\">https://doi.org/10.15479/AT-ISTA-20777</a>"},"title":"Scale-free activity as a basis for spatial learning and memory in the brain","project":[{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"}],"date_updated":"2026-07-24T08:14:37Z","day":"11","file_date_updated":"2026-06-11T22:30:02Z","year":"2025","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"date_published":"2025-12-11T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"has_accepted_license":"1","oa":1,"status":"public","month":"12","corr_author":"1","ddc":["570","539","571"],"page":"104","date_created":"2025-12-10T19:37:41Z","_id":"20777","OA_place":"publisher","degree_awarded":"PhD","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n","lang":"eng"}],"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"},{"pmid":1,"APC_amount":"7068 EUR","related_material":{"link":[{"description":"News on ISTA website","relation":"research_data","url":"https://ista.ac.at/en/news/the-shadow-of-an-electron/"}],"record":[{"status":"public","relation":"research_data","id":"19409"},{"relation":"dissertation_contains","status":"public","id":"19836"}]},"external_id":{"isi":["001475587400022"],"pmid":["40274808"],"arxiv":["2408.03224"]},"DOAJ_listed":"1","oa_version":"Published Version","doi":"10.1038/s41467-025-58969-y","author":[{"id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","last_name":"Jirovec","full_name":"Jirovec, Daniel"},{"last_name":"Schell","full_name":"Schell, Yona A","first_name":"Yona A","id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Rimbach-Russ, Maximilian","last_name":"Rimbach-Russ","first_name":"Maximilian"},{"first_name":"Stefano","last_name":"Bosco","full_name":"Bosco, Stefano"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"file":[{"date_created":"2025-05-05T07:08:23Z","success":1,"date_updated":"2025-05-05T07:08:23Z","file_name":"2025_NatureComm_SaezMollejo.pdf","creator":"dernst","content_type":"application/pdf","file_size":1548756,"file_id":"19645","relation":"main_file","access_level":"open_access","checksum":"13fe84cddc9d4e47213bf17acdac70d7"}],"intvolume":"        16","publication_status":"published","article_number":"3862","arxiv":1,"volume":16,"project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"citation":{"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).","mla":"Saez Mollejo, Jaime, et al. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>, vol. 16, 3862, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>.","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.","chicago":"Saez Mollejo, Jaime, Daniel Jirovec, Yona A Schell, Josip Kukucka, Stefano Calcaterra, Daniel Chrastina, Giovanni Isella, Maximilian Rimbach-Russ, Stefano Bosco, and Georgios Katsaros. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>.","apa":"Saez Mollejo, J., Jirovec, D., Schell, Y. A., Kukucka, J., Calcaterra, S., Chrastina, D., … Katsaros, G. (2025). Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-58969-y\">https://doi.org/10.1038/s41467-025-58969-y</a>","ama":"Saez Mollejo J, Jirovec D, Schell YA, et al. Exchange anisotropies in microwave-driven singlet-triplet qubits. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-58969-y\">10.1038/s41467-025-58969-y</a>","ieee":"J. Saez Mollejo <i>et al.</i>, “Exchange anisotropies in microwave-driven singlet-triplet qubits,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"title":"Exchange anisotropies in microwave-driven singlet-triplet qubits","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","department":[{"_id":"GeKa"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-04-24T00:00:00Z","type":"journal_article","year":"2025","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2026-09-05T22:31:03Z","day":"24","file_date_updated":"2025-05-05T07:08:23Z","ddc":["530"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"isi":1,"corr_author":"1","oa":1,"status":"public","publication":"Nature Communications","month":"04","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_type":"original","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."}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2025-03-19T13:28:12Z","_id":"19424","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher"},{"oa_version":"Published Version","doi":"10.15479/AT-ISTA-19836","author":[{"first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime"}],"file":[{"embargo_to":"open_access","date_created":"2025-06-16T09:38:49Z","date_updated":"2026-04-01T22:30:07Z","creator":"jsaezmol","file_name":"istaustriathesis-master - Copy.zip","content_type":"application/x-zip-compressed","file_size":59892829,"file_id":"19849","access_level":"closed","relation":"source_file","checksum":"643bfddead59857536cce4d57c775b32"},{"checksum":"e3dcb767fcc2b1787a455fdda991cefb","embargo":"2026-04-01","file_size":22382376,"file_id":"19851","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"jsaezmol","file_name":"SaezMollejo_PhDFinal_pdfa-1b.pdf","date_created":"2025-06-18T08:50:16Z","date_updated":"2026-04-01T22:30:07Z"}],"related_material":{"record":[{"id":"19424","status":"public","relation":"part_of_dissertation"}]},"doi_confirm":"1","publication_status":"published","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"language":[{"iso":"eng"}],"date_published":"2025-06-13T00:00:00Z","type":"dissertation","year":"2025","publication_identifier":{"issn":["2663-337X"]},"day":"13","date_updated":"2026-07-29T12:55:59Z","file_date_updated":"2026-04-01T22:30:07Z","project":[{"name":"Integrated Germanium Quantum Technology","grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"_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"},{"name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"citation":{"apa":"Saez Mollejo, J. (2025). <i>Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>","ama":"Saez Mollejo J. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>","chicago":"Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>.","ieee":"J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.","short":"J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.","mla":"Saez Mollejo, Jaime. <i>Singlet-Triplet Qubits in Planar Germanium: From Exchange Anisotropies to Autonomous Tuning </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>.","ista":"Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria."},"title":"Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning ","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","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"}],"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","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","page":"175","date_created":"2025-06-13T09:01:50Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"19836","OA_place":"publisher","ddc":["530","539"],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","status":"public","oa":1,"month":"06"},{"publication_status":"published","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT-ISTA-20563","file":[{"date_created":"2025-11-17T21:04:15Z","date_updated":"2026-01-01T23:30:03Z","file_name":"2025_quattrocchi_filippo_thesis.pdf","creator":"fquattro","embargo":"2026-01-01","checksum":"6f55275bdf99992be3a6457d949dd664","access_level":"open_access","relation":"main_file","file_size":4326411,"file_id":"20653","content_type":"application/pdf"},{"checksum":"707e580f5d993a214c0dba456b75837b","content_type":"application/zip","file_size":11726509,"file_id":"20654","relation":"source_file","access_level":"closed","creator":"fquattro","file_name":"2025_quattrocchi_thesis.zip","date_created":"2025-11-17T21:05:43Z","date_updated":"2026-01-01T23:30:03Z","embargo_to":"open_access"}],"author":[{"first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931","full_name":"Quattrocchi, Filippo"}],"oa_version":"Published Version","related_material":{"record":[{"id":"20569","status":"public","relation":"part_of_dissertation"},{"id":"20571","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"20570"},{"id":"18706","status":"public","relation":"part_of_dissertation"}]},"keyword":["optimal transport","kinetic equations","boundary value problems","quantization","gradient flows","homogenization"],"degree_awarded":"PhD","date_created":"2025-10-28T13:10:49Z","page":"240","_id":"20563","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","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.","supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","status":"public","oa":1,"month":"11","ddc":["515","519"],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","day":"03","date_updated":"2026-07-23T06:09:20Z","file_date_updated":"2026-01-01T23:30:03Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"date_published":"2025-11-03T00:00:00Z","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","project":[{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Differential Systems","grant_number":"F06504"}],"citation":{"ieee":"F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025.","ama":"Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>","chicago":"Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>.","apa":"Quattrocchi, F. (2025). <i>Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>","short":"F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025.","mla":"Quattrocchi, Filippo. <i>Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>.","ista":"Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria."},"title":"Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures"},{"arxiv":1,"article_number":"2502.15665","publication_status":"draft","doi":"10.48550/arXiv.2502.15665","author":[{"first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","last_name":"Brigati","full_name":"Brigati, Giovanni"},{"full_name":"Maas, Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931","full_name":"Quattrocchi, Filippo"}],"oa_version":"Preprint","external_id":{"arxiv":["2502.15665"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20563"}]},"keyword":["optimal transport","kinetic theory","second-order discrepancy","Vlasov equation","Wasserstein splines."],"date_created":"2025-10-28T13:12:08Z","_id":"20569","OA_place":"repository","abstract":[{"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.","lang":"eng"}],"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.","ec_funded":1,"corr_author":"1","status":"public","oa":1,"month":"08","publication":"arXiv","year":"2025","type":"preprint","day":"10","date_updated":"2026-09-05T22:31:05Z","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"language":[{"iso":"eng"}],"date_published":"2025-08-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2502.15665","open_access":"1"}],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"citation":{"ieee":"G. Brigati, J. Maas, and F. Quattrocchi, “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures,” <i>arXiv</i>. .","chicago":"Brigati, Giovanni, Jan Maas, and Filippo Quattrocchi. “Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-Order Discrepancies between Probability Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>.","apa":"Brigati, G., Maas, J., &#38; Quattrocchi, F. (n.d.). Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2502.15665\">https://doi.org/10.48550/arXiv.2502.15665</a>","ama":"Brigati G, Maas J, Quattrocchi F. Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>","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.” <i>ArXiv</i>, 2502.15665, doi:<a href=\"https://doi.org/10.48550/arXiv.2502.15665\">10.48550/arXiv.2502.15665</a>.","short":"G. Brigati, J. Maas, F. Quattrocchi, ArXiv (n.d.)."},"title":"Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures"},{"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2025-06-26T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"year":"2025","date_updated":"2026-07-29T12:55:31Z","day":"26","file_date_updated":"2025-12-27T23:30:02Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"citation":{"ama":"Suresh SS. Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>","apa":"Suresh, S. S. (2025). <i>Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>","chicago":"Suresh, Sarath S. “Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>.","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.","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.","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. <i>Turbulence in Polymeric Flows: A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>."},"title":"Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","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.","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"}],"ec_funded":1,"supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_created":"2025-06-26T08:39:08Z","page":"82","OA_place":"publisher","tmp":{"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)","image":"/images/cc_by_nc_sa.png"},"_id":"19906","ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"}],"corr_author":"1","status":"public","oa":1,"month":"06","oa_version":"Published Version","doi":"10.15479/AT-ISTA-19906","author":[{"full_name":"Suresh, Sarath S","last_name":"Suresh","id":"3D126CC4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarath S"}],"file":[{"creator":"cchlebak","file_name":"Thesis_v9_PDFA2b.pdf","date_created":"2025-06-26T08:40:53Z","date_updated":"2025-12-27T23:30:02Z","content_type":"application/pdf","file_size":6504571,"file_id":"19907","relation":"main_file","access_level":"open_access","embargo":"2025-12-27","checksum":"302a07605a9e64ac247c2036d5f5b1cd"},{"access_level":"closed","relation":"source_file","file_id":"19908","file_size":59092991,"content_type":"application/x-zip-compressed","checksum":"5d69d10bdacc24c27f02924379405bd9","file_name":"Thesis Template - ISTA [istaustriathesis].zip","creator":"cchlebak","embargo_to":"open_access","date_updated":"2025-12-27T23:30:02Z","date_created":"2025-06-26T08:41:24Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10299"}]},"doi_confirm":"1","publication_status":"published","alternative_title":["ISTA Thesis"]},{"language":[{"iso":"eng"}],"date_published":"2025-04-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"has_accepted_license":"1","day":"1","date_updated":"2026-08-12T08:45:39Z","file_date_updated":"2025-10-11T22:30:02Z","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","year":"2025","citation":{"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. <i>Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>.","short":"R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","ama":"Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>","apa":"Sett, R. (2025). <i>Quantum remote sensing and non-equilibrium phase transitions in the microwave regime</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>","chicago":"Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>.","ieee":"R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025."},"title":"Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","project":[{"name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supervisor":[{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","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.","abstract":[{"text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n","lang":"eng"}],"ec_funded":1,"page":"109","date_created":"2025-04-09T16:44:26Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","_id":"19533","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"],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"ddc":["530"],"status":"public","oa":1,"month":"04","corr_author":"1","oa_version":"Published Version","file":[{"date_created":"2025-04-10T11:33:22Z","date_updated":"2025-10-11T22:30:02Z","creator":"rsett","file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","content_type":"application/pdf","file_size":4129208,"file_id":"19538","access_level":"open_access","relation":"main_file","embargo":"2025-10-11","checksum":"ba6cd2289d0141a160a14fc97df1632f"},{"file_name":"PhD Thesis Riya Sett.zip","creator":"rsett","date_updated":"2025-10-11T22:30:02Z","date_created":"2025-04-10T11:34:08Z","embargo_to":"open_access","checksum":"ee63a94cb8f7adf5e766903028b81ed6","content_type":"application/x-zip-compressed","file_id":"19539","file_size":6646110,"access_level":"closed","relation":"source_file"}],"author":[{"first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya"}],"doi":"10.15479/AT-ISTA-19533","doi_confirm":"1","related_material":{"record":[{"id":"18978","relation":"research_data","status":"public"},{"id":"19280","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17183"},{"id":"13117","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","alternative_title":["ISTA Thesis"]}]