[{"month":"04","oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"oa":1,"publication_identifier":{"issn":["2791-4585"]},"date_published":"2023-04-05T00:00:00Z","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"date_created":"2023-04-06T06:09:40Z","file_size":52795,"checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"Dispersaldata.xlsx","relation":"supplementary_material","access_level":"closed","file_id":"12805","creator":"mjulseth"},{"creator":"mjulseth","file_id":"12806","relation":"supplementary_material","access_level":"open_access","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","content_type":"application/vnd.wolfram.nb","date_updated":"2023-06-02T22:30:04Z","checksum":"5a13b6d204371572e249f03795bc0d04","file_size":787239,"embargo":"2023-06-01","date_created":"2023-04-06T06:11:27Z"},{"access_level":"closed","relation":"source_file","creator":"mjulseth","file_id":"12812","embargo_to":"open_access","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_size":1061763,"date_created":"2023-04-06T08:26:12Z","file_name":"ThesisMaraJulseth_04_23.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-06-02T22:30:04Z"},{"access_level":"open_access","relation":"main_file","file_id":"12813","creator":"mjulseth","embargo":"2023-06-01","date_created":"2023-04-06T08:26:37Z","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_size":1741364,"date_updated":"2023-06-02T22:30:04Z","content_type":"application/pdf","file_name":"ThesisMaraJulseth_04_23.pdf"}],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","alternative_title":["ISTA Master's Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2023-04-04T18:57:11Z","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","full_name":"Julseth, Mara","first_name":"Mara","last_name":"Julseth"}],"_id":"12800","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-06-02T22:30:04Z","page":"21","abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"degree_awarded":"MS","doi":"10.15479/at:ista:12800","day":"05","date_updated":"2023-06-02T22:30:05Z","year":"2023","citation":{"ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>"},"ddc":["576"]},{"file":[{"creator":"cchlebak","file_id":"12814","access_level":"closed","relation":"main_file","content_type":"application/pdf","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_updated":"2023-04-07T06:16:06Z","file_size":9881969,"checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo_to":"open_access","embargo":"2024-04-07","date_created":"2023-04-07T06:16:06Z"},{"access_level":"closed","relation":"source_file","file_id":"12815","creator":"cchlebak","date_created":"2023-04-07T06:17:11Z","checksum":"81198f63c294890f6d58e8b29782efdc","file_size":44201583,"date_updated":"2023-04-07T06:17:11Z","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","content_type":"application/pdf"},{"relation":"source_file","access_level":"closed","creator":"cchlebak","file_id":"12816","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_size":84731244,"date_created":"2023-04-07T06:18:05Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_CatarinaAlcarva_final.docx","date_updated":"2023-04-07T06:18:05Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","date_published":"2023-04-06T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"oa_version":"Published Version","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"month":"04","ddc":["570"],"date_updated":"2023-04-26T12:16:56Z","year":"2023","citation":{"ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria."},"degree_awarded":"PhD","doi":"10.15479/at:ista:12809","day":"06","abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"page":"115","file_date_updated":"2023-04-07T06:18:05Z","publisher":"Institute of Science and Technology Austria","_id":"12809","author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina","first_name":"Catarina","last_name":"Alcarva"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RySh"}],"article_processing_charge":"No","date_created":"2023-04-06T07:54:09Z","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","alternative_title":["ISTA Thesis"]},{"publisher":"Institute of Science and Technology Austria","page":"106","ec_funded":1,"file_date_updated":"2023-04-20T09:26:51Z","publication_status":"published","article_processing_charge":"No","date_created":"2023-04-14T14:56:04Z","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","_id":"12826","author":[{"last_name":"Pokusaeva","first_name":"Victoria","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570","571"],"degree_awarded":"PhD","doi":"10.15479/at:ista:12826","day":"18","abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"date_updated":"2023-06-23T09:47:36Z","citation":{"mla":"Pokusaeva, Victoria. <i>Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","apa":"Pokusaeva, V. (2023). <i>Neural control of optic flow-based navigation in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023."},"year":"2023","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"month":"04","has_accepted_license":"1","file":[{"access_level":"closed","relation":"source_file","file_id":"12857","creator":"vpokusae","date_created":"2023-04-20T09:14:38Z","file_size":14507243,"checksum":"5f589a9af025f7eeebfd0c186209913e","date_updated":"2023-04-20T09:26:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Pokusaeva.docx"},{"file_id":"12858","creator":"vpokusae","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2023-04-20T09:14:44Z","content_type":"application/pdf","file_name":"Thesis_Pokusaeva.pdf","date_created":"2023-04-20T09:14:44Z","file_size":10090711,"checksum":"bbeed76db45a996b4c91a9abe12ce0ec"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-04-18T00:00:00Z","type":"dissertation"},{"oa":1,"abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"day":"25","doi":"10.48550/arXiv.2303.14555","arxiv":1,"type":"preprint","external_id":{"arxiv":["2303.14555"]},"date_published":"2023-03-25T00:00:00Z","citation":{"chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>.","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” <i>arXiv</i>. .","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>","apa":"Chern, A., &#38; Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, 2303.14555, doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>.","short":"A. Chern, S. Ishida, ArXiv (n.d.)."},"year":"2023","date_updated":"2023-04-25T06:51:21Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","article_number":"2303.14555","title":"Area formula for spherical polygons via prequantization","month":"03","date_created":"2023-04-18T19:16:06Z","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"submitted","oa_version":"Preprint","author":[{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"},{"first_name":"Sadashige","last_name":"Ishida","full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"}],"publication":"arXiv","_id":"12846","language":[{"iso":"eng"}]},{"publication":"Proceedings of the 40th International Conference on Machine Learning","month":"10","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"conference":{"location":"Honolulu, HI, United States","end_date":"2023-07-29","start_date":"2023-07-23","name":"ICML: International Conference on Machine Learning"},"type":"conference","date_published":"2023-10-27T00:00:00Z","oa":1,"related_material":{"link":[{"url":"https://github.com/simone-bombari/beyond-universal-robustness","relation":"software"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"author":[{"first_name":"Simone","last_name":"Bombari","full_name":"Bombari, Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa"},{"id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","last_name":"Kiyani","first_name":"Shayan","full_name":"Kiyani, Shayan"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"_id":"12859","intvolume":"       202","title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","alternative_title":["PMLR"],"date_created":"2023-04-23T16:11:03Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"publication_status":"published","quality_controlled":"1","page":"2738-2776","publisher":"ML Research Press","external_id":{"arxiv":["2302.01629"]},"citation":{"ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 2738–76.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:2738–76. ML Research Press, 2023.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","apa":"Bombari, S., Kiyani, S., &#38; Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:2738-2776."},"year":"2023","date_updated":"2024-09-10T13:03:19Z","abstract":[{"lang":"eng","text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10)."}],"day":"27","arxiv":1,"volume":202,"acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n"},{"type":"research_data","date_published":"2023-04-26T00:00:00Z","citation":{"mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. <i>Research Data for: A Stochastic Cellular Automaton Model of Culture Formation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","short":"F.R. Klausen, A.B. Lauritsen, (2023).","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>."},"year":"2023","date_updated":"2023-11-13T07:47:29Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"oa":1,"abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage.  We first analyse the model  with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. "}],"day":"26","doi":"10.15479/AT:ISTA:12869","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"14505","status":"for_moderation"},{"status":"public","relation":"used_in_publication","id":"12890"}]},"ddc":["000"],"file":[{"date_updated":"2023-04-26T12:30:06Z","content_type":"application/octet-stream","file_name":"README.md","date_created":"2023-04-26T12:30:06Z","checksum":"85ede12d38bb8d944022a8cba4d719f5","file_size":4567,"file_id":"12870","creator":"alaurits","access_level":"open_access","relation":"main_file","success":1},{"success":1,"access_level":"open_access","relation":"main_file","creator":"alaurits","file_id":"12871","checksum":"25bf79452ae895f9c8a20571a096b4c3","file_size":732586731,"date_created":"2023-04-26T12:27:34Z","file_name":"simulations_era=10_flux_varied_europe.zip","content_type":"application/x-zip-compressed","date_updated":"2023-04-26T12:27:34Z"},{"date_created":"2023-04-26T12:29:53Z","file_size":1743893150,"checksum":"bca48d80ece73eb169aee7211a4a751a","date_updated":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","success":1,"file_id":"12872","creator":"alaurits"},{"date_updated":"2023-04-26T12:29:19Z","file_name":"simulations_era=10_R_varied_torus.zip","content_type":"application/x-zip-compressed","date_created":"2023-04-26T12:29:19Z","file_size":878391851,"checksum":"e77a655db15486a387a36362fbf0b665","file_id":"12873","creator":"alaurits","success":1,"access_level":"open_access","relation":"main_file"},{"date_updated":"2023-04-26T12:30:05Z","content_type":"application/x-zip-compressed","file_name":"simulations_era=100.zip","date_created":"2023-04-26T12:30:05Z","file_size":201652478,"checksum":"8556406513adc4aa2e0417f46680f627","file_id":"12874","creator":"alaurits","relation":"main_file","access_level":"open_access","success":1}],"acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","author":[{"full_name":"Klausen, Frederik Ravn","last_name":"Klausen","first_name":"Frederik Ravn"},{"last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","_id":"12869","month":"04","title":"Research data for: A stochastic cellular automaton model of culture formation","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_created":"2023-04-26T12:34:49Z","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-04-26T12:30:06Z","publisher":"Institute of Science and Technology Austria"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"04","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","related_material":{"record":[{"id":"10806","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10042","relation":"part_of_dissertation"},{"id":"12237","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9118","relation":"part_of_dissertation"},{"status":"public","id":"10123","relation":"part_of_dissertation"}]},"file":[{"file_id":"12887","creator":"mcalcabr","relation":"source_file","access_level":"closed","date_updated":"2023-05-02T07:43:18Z","file_name":"Thesis_Calcabrini.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-05-02T07:43:18Z","checksum":"9347b0e09425f56fdcede5d3528404dc","file_size":99627036},{"access_level":"open_access","success":1,"relation":"main_file","creator":"mcalcabr","file_id":"12888","file_size":8742220,"checksum":"2d188b76621086cd384f0b9264b0a576","date_created":"2023-05-02T07:42:45Z","file_name":"Thesis_Calcabrini_pdfa.pdf","content_type":"application/pdf","date_updated":"2023-05-02T07:42:45Z"}],"type":"dissertation","date_published":"2023-04-28T00:00:00Z","oa":1,"supervisor":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria"}],"publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"file_date_updated":"2023-05-02T07:43:18Z","ec_funded":1,"page":"82","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Calcabrini","first_name":"Mariano","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"}],"_id":"12885","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"date_created":"2023-05-02T07:58:57Z","publication_status":"published","ddc":["546","541"],"citation":{"ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>."},"year":"2023","date_updated":"2023-08-14T07:25:26Z","abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"day":"28","doi":"10.15479/at:ista:12885","degree_awarded":"PhD"},{"language":[{"iso":"eng"}],"article_number":"054307","month":"11","oa_version":"Preprint","publication":"Physical Review E","status":"public","related_material":{"link":[{"url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation","relation":"software"}],"record":[{"relation":"research_data","id":"12869","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"type":"journal_article","date_published":"2023-11-08T00:00:00Z","article_type":"original","publisher":"American Physical Society","quality_controlled":"1","intvolume":"       108","title":"Stochastic cellular automaton model of culture formation","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_created":"2023-05-04T08:35:01Z","publication_status":"published","issue":"5","author":[{"full_name":"Klausen, Frederik Ravn","last_name":"Klausen","first_name":"Frederik Ravn"},{"first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"scopus_import":"1","_id":"12890","acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","volume":108,"abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders."}],"day":"08","doi":"10.1103/PhysRevE.108.054307","arxiv":1,"external_id":{"arxiv":["2305.02153"]},"citation":{"ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023)."},"year":"2023","date_updated":"2023-11-13T07:47:30Z"},{"ddc":["570"],"year":"2023","citation":{"apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria."},"date_updated":"2023-08-21T06:25:48Z","day":"05","doi":"10.15479/at:ista:12891","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"ec_funded":1,"page":"190","file_date_updated":"2023-05-05T13:04:15Z","publisher":"Institute of Science and Technology Austria","_id":"12891","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"date_created":"2023-05-05T08:48:20Z","publication_status":"published","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","alternative_title":["ISTA Thesis"],"file":[{"file_id":"12907","creator":"aschauer","relation":"main_file","access_level":"closed","date_updated":"2023-05-05T13:01:14Z","file_name":"Thesis_Schauer_final.pdf","content_type":"application/pdf","date_created":"2023-05-05T13:01:14Z","embargo":"2024-05-05","embargo_to":"open_access","file_size":31434230,"checksum":"59b0303dc483f40a96a610a90aab7ee9"},{"relation":"source_file","access_level":"closed","creator":"aschauer","file_id":"12908","checksum":"25f54e12479b6adaabd129a20568e6c1","file_size":43809109,"date_created":"2023-05-05T13:04:15Z","file_name":"Thesis_Schauer_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-05-05T13:04:15Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8966","status":"public"},{"relation":"part_of_dissertation","id":"7888","status":"public"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","date_published":"2023-05-05T00:00:00Z","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","month":"05"},{"oa":1,"supervisor":[{"first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"type":"dissertation","date_published":"2023-05-05T00:00:00Z","status":"public","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9817"},{"status":"public","relation":"part_of_dissertation","id":"7117"},{"status":"public","relation":"dissertation_contains","id":"13188"}]},"file":[{"date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-hafner-2023may11-a2b.pdf","content_type":"application/pdf","date_created":"2023-05-11T10:43:20Z","embargo":"2023-12-07","file_size":50714445,"checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","file_id":"12942","creator":"chafner","access_level":"open_access","relation":"main_file"},{"date_created":"2023-05-11T10:43:44Z","embargo_to":"open_access","checksum":"a6b51334be2b81672357b1549afab40c","file_size":265319,"date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-release-form.pdf","content_type":"application/pdf","access_level":"closed","relation":"source_file","file_id":"12943","creator":"chafner"}],"month":"05","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"day":"05","degree_awarded":"PhD","doi":"10.15479/at:ista:12897","citation":{"ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria."},"year":"2023","date_updated":"2024-01-29T10:47:51Z","ddc":["516","004","518","531"],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","alternative_title":["ISTA Thesis"],"date_created":"2023-05-05T10:40:14Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publication_status":"published","author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"}],"_id":"12897","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-12-08T23:30:04Z","ec_funded":1,"page":"180"},{"file":[{"file_id":"12928","creator":"rsahu","relation":"source_file","access_level":"closed","date_updated":"2023-06-06T22:30:03Z","file_name":"thesis.zip","content_type":"application/x-zip-compressed","date_created":"2023-05-09T08:45:14Z","embargo_to":"open_access","checksum":"8cbdab9c37ee55e591092a6f66b272c4","file_size":36767177},{"date_updated":"2023-07-06T11:37:40Z","content_type":"application/pdf","file_name":"thesis_pdfa_final.pdf","date_created":"2023-05-09T08:51:17Z","checksum":"439659ead46618147309be39d9dd5a8c","file_size":17501990,"file_id":"12929","creator":"rsahu","access_level":"closed","relation":"main_file"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9114"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"status":"public","id":"13175","relation":"new_edition"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2023-05-05T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"month":"05","has_accepted_license":"1","ddc":["537","535","539"],"degree_awarded":"PhD","doi":"10.15479/at:ista:12900","day":"05","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"date_updated":"2024-10-29T09:11:05Z","citation":{"ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>."},"year":"2023","publisher":"Institute of Science and Technology Austria","page":"190","ec_funded":1,"file_date_updated":"2023-07-06T11:37:40Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"article_processing_charge":"No","date_created":"2023-05-05T11:08:50Z","title":"Cavity quantum electrooptics","alternative_title":["ISTA Thesis"],"_id":"12900","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162"}]},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-05-11T12:50:18Z","contributor":[{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-10T10:00:49Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"article_processing_charge":"No","oa_version":"Published Version","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","month":"05","has_accepted_license":"1","_id":"12933","author":[{"first_name":"Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"gpuixeus","file_id":"12934","relation":"main_file","success":1,"access_level":"open_access","content_type":"text/csv","file_name":"Dataset_S1.csv","date_updated":"2023-05-10T09:41:43Z","checksum":"0ba0bcd0bb8b18d84792136a4370df90","file_size":8029982,"date_created":"2023-05-10T09:41:43Z"},{"checksum":"a62aa9a6d4904e0fdb699cf752640863","file_size":13667640,"date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S2.csv","content_type":"text/csv","date_updated":"2023-05-10T09:41:43Z","success":1,"access_level":"open_access","relation":"main_file","creator":"gpuixeus","file_id":"12935"},{"checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","file_size":8369141,"date_created":"2023-05-10T09:41:48Z","content_type":"text/csv","file_name":"Dataset_S3.csv","date_updated":"2023-05-10T09:41:48Z","success":1,"relation":"main_file","access_level":"open_access","creator":"gpuixeus","file_id":"12936"},{"file_size":19543247,"checksum":"f6156e5fc44446c907ddd0d7289d4cf8","date_created":"2023-05-10T09:41:50Z","file_name":"Dataset_S4.csv","content_type":"text/csv","date_updated":"2023-05-10T09:41:50Z","access_level":"open_access","success":1,"relation":"main_file","creator":"gpuixeus","file_id":"12937"},{"date_updated":"2023-05-11T12:50:18Z","content_type":"text/plain","file_name":"readme.txt","date_created":"2023-05-11T12:50:18Z","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_size":4566,"file_id":"12944","creator":"gpuixeus","relation":"main_file","access_level":"open_access","success":1}],"ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"14058","status":"public"},{"relation":"used_in_publication","id":"14077","status":"public"}]},"day":"15","doi":"10.15479/AT:ISTA:12933","oa":1,"abstract":[{"lang":"eng","text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\"."}],"year":"2023","citation":{"ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","mla":"Puixeu Sala, Gemma. <i>Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","short":"G. Puixeu Sala, (2023).","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>.","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>"},"date_updated":"2023-12-13T12:15:36Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"research_data","date_published":"2023-05-15T00:00:00Z"},{"file":[{"file_id":"12988","creator":"dboocock","access_level":"closed","relation":"main_file","date_updated":"2023-05-19T07:04:25Z","content_type":"application/pdf","file_name":"thesis_boocock.pdf","embargo":"2024-05-17","date_created":"2023-05-17T13:39:54Z","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","file_size":40414730,"embargo_to":"open_access"},{"creator":"dboocock","file_id":"12989","access_level":"closed","relation":"source_file","file_name":"thesis_boocock.zip","content_type":"application/zip","date_updated":"2023-05-17T14:35:13Z","checksum":"581a2313ffeb40fe77e8a122a25a7795","file_size":34338567,"date_created":"2023-05-17T13:39:53Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"8602","relation":"part_of_dissertation"}]},"status":"public","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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","date_published":"2023-05-17T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"oa_version":"Published Version","month":"05","ddc":["530"],"citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>","apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>"},"year":"2023","date_updated":"2023-08-04T11:02:40Z","day":"17","doi":"10.15479/at:ista:12964","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"ec_funded":1,"page":"146","file_date_updated":"2023-05-19T07:04:25Z","publisher":"Institute of Science and Technology Austria","_id":"12964","author":[{"full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-15T14:52:36Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Mechanochemical pattern formation across biological scales"},{"date_published":"2023-07-26T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"a0b0ba3b36f43a94388e8824613d812a","file_size":78940724,"date_created":"2023-06-19T11:02:23Z","content_type":"application/pdf","file_name":"2023_ACMToG_Freire.pdf","date_updated":"2023-06-19T11:02:23Z","access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","file_id":"13156"},{"success":1,"access_level":"open_access","relation":"main_file","file_id":"13157","creator":"dernst","date_created":"2023-06-20T12:20:51Z","file_size":34345905,"checksum":"b9206bbb67af82df49b7e7cdbde3410c","date_updated":"2023-06-20T12:20:51Z","content_type":"application/pdf","file_name":"2023_ACMToG_SuppMaterial_Freire.pdf"}],"publication":"Transactions on Graphics","has_accepted_license":"1","month":"07","article_number":"142","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"}],"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"keyword":["PCB design and layout","Mesh geometry models"],"conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2023-08-06","end_date":"2023-08-10","location":"Los Angeles, CA, United States"},"isi":1,"external_id":{"isi":["001044671300108"]},"date_updated":"2024-01-29T10:30:49Z","year":"2023","citation":{"ieee":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre, “PCBend: Light up your 3D shapes with foldable circuit boards,” <i>Transactions on Graphics</i>, vol. 42, no. 4. Association for Computing Machinery, 2023.","chicago":"Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron, Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” <i>Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3592411\">https://doi.org/10.1145/3592411</a>.","ama":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend: Light up your 3D shapes with foldable circuit boards. <i>Transactions on Graphics</i>. 2023;42(4). doi:<a href=\"https://doi.org/10.1145/3592411\">10.1145/3592411</a>","apa":"Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., &#38; Lefebvre, S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. <i>Transactions on Graphics</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3592411\">https://doi.org/10.1145/3592411</a>","ista":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 42(4), 142.","mla":"Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” <i>Transactions on Graphics</i>, vol. 42, no. 4, 142, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3592411\">10.1145/3592411</a>.","short":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre, Transactions on Graphics 42 (2023)."},"abstract":[{"text":"We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. \r\nOur approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.\r\nOur technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs.","lang":"eng"}],"doi":"10.1145/3592411","day":"26","ddc":["006"],"acknowledgement":"We thank the reviewers for the valuable feedback. We also thank the Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication and assembly. This project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 715767 – MATERIALIZABLE).","volume":42,"author":[{"full_name":"Freire, Marco","first_name":"Marco","last_name":"Freire"},{"orcid":"0009-0007-6138-6890","full_name":"Bhargava, Manas","first_name":"Manas","last_name":"Bhargava","id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425"},{"full_name":"Schreck, Camille","last_name":"Schreck","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hugron, Pierre-Alexandre","first_name":"Pierre-Alexandre","last_name":"Hugron"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lefebvre, Sylvain","first_name":"Sylvain","last_name":"Lefebvre"}],"issue":"4","_id":"13049","title":"PCBend: Light up your 3D shapes with foldable circuit boards","intvolume":"        42","publication_status":"published","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"date_created":"2023-05-22T08:37:04Z","file_date_updated":"2023-06-20T12:20:51Z","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Association for Computing Machinery"},{"volume":495,"acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","researchdata_availability":"upon request","citation":{"mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>, vol. 495, 117168, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023).","ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., &#38; Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). <i>International Journal of Mass Spectrometry</i>. 2023;495. doi:<a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">10.1016/j.ijms.2023.117168</a>","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” <i>International Journal of Mass Spectrometry</i>, vol. 495. Elsevier, 2023.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” <i>International Journal of Mass Spectrometry</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ijms.2023.117168\">https://doi.org/10.1016/j.ijms.2023.117168</a>."},"year":"2023","date_updated":"2026-03-02T09:38:59Z","day":"23","doi":"10.1016/j.ijms.2023.117168","abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"quality_controlled":"1","publisher":"Elsevier","article_type":"original","scopus_import":"1","_id":"14653","dataavailabilitystatement":"Data will be made available on request.","author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","first_name":"Florian","full_name":"Kluibenschedl, Florian"},{"full_name":"Ploner, Anna","last_name":"Ploner","first_name":"Anna"},{"last_name":"Meisenbichler","first_name":"Christina","full_name":"Meisenbichler, Christina"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"},{"first_name":"Thomas","last_name":"Müller","full_name":"Müller, Thomas"}],"department":[{"_id":"GradSch"}],"date_created":"2023-12-10T23:00:57Z","article_processing_charge":"Yes (in subscription journal)","publication_status":"epub_ahead","intvolume":"       495","title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ijms.2023.117168"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","status":"public","type":"journal_article","date_published":"2023-11-23T00:00:00Z","publication_identifier":{"issn":["1387-3806"]},"oa":1,"language":[{"iso":"eng"}],"publication":"International Journal of Mass Spectrometry","oa_version":"Published Version","article_number":"117168","month":"11"},{"file":[{"creator":"oolusany","file_id":"10659","access_level":"open_access","relation":"main_file","file_name":"rstb.2021.0010.pdf","content_type":"application/pdf","date_updated":"2022-01-24T10:34:45Z","checksum":"04ca9e2f0e344d680b947f2457df8d0a","file_size":1845792,"date_created":"2022-01-24T10:34:45Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","id":"14711","relation":"dissertation_contains"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.08.05.455207"}]},"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-01-24T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"month":"01","article_number":"20210010","publication":"Philosophical Transactions of the Royal Society B","has_accepted_license":"1","volume":377,"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","ddc":["576"],"doi":"10.1098/rstb.2021.0010","day":"24","abstract":[{"lang":"eng","text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’."}],"date_updated":"2025-05-26T09:05:09Z","citation":{"chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>.","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846. The Royal Society, 2022.","apa":"Sachdeva, H., Olusanya, O. O., &#38; Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0010\">https://doi.org/10.1098/rstb.2021.0010</a>","ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. <i>Philosophical Transactions of the Royal Society B</i>. 2022;377(1846). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>","ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022).","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” <i>Philosophical Transactions of the Royal Society B</i>, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0010\">10.1098/rstb.2021.0010</a>."},"year":"2022","isi":1,"external_id":{"pmid":["35067097"],"isi":["000745854300008"]},"publisher":"The Royal Society","article_type":"original","quality_controlled":"1","file_date_updated":"2022-01-24T10:34:45Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2022-01-24T10:34:53Z","title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","intvolume":"       377","_id":"10658","pmid":1,"author":[{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"first_name":"Oluwafunmilola O","last_name":"Olusanya","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"issue":"1846"},{"oa":1,"supervisor":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2022-02-07T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"date_created":"2022-02-04T15:36:12Z","embargo_to":"open_access","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","file_size":6757886,"date_updated":"2023-02-03T23:30:03Z","file_name":"Thesis_Sina_Metzler.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"10728","creator":"smetzler"},{"file_id":"10730","creator":"smetzler","relation":"main_file","access_level":"open_access","date_updated":"2023-02-03T23:30:03Z","file_name":"Thesis_Sina_Metzler_A2.pdf","content_type":"application/pdf","embargo":"2023-02-02","date_created":"2022-02-04T15:36:43Z","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_size":6314921},{"checksum":"dedd14b7be7a75d63018dbfc68dd8113","file_size":6882557,"embargo":"2023-02-02","date_created":"2022-02-07T10:35:02Z","file_name":"Thesis_Sina_Metzler_print.pdf","content_type":"application/pdf","date_updated":"2023-02-04T23:30:03Z","relation":"main_file","access_level":"open_access","creator":"smetzler","file_id":"10742"}],"month":"02","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history."}],"day":"07","doi":"10.15479/AT:ISTA:10727","degree_awarded":"PhD","citation":{"ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>"},"year":"2022","date_updated":"2023-09-07T13:43:23Z","ddc":["570"],"title":"Pathogen-mediated sexual selection and immunization in ant colonies","alternative_title":["ISTA Thesis"],"date_created":"2022-02-04T15:45:12Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publication_status":"published","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler","first_name":"Sina"}],"_id":"10727","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-02-04T23:30:03Z","ec_funded":1},{"_id":"10759","author":[{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-02-16T13:27:37Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Analytic and machine learning approaches to composite quantum impurities","ec_funded":1,"page":"120","file_date_updated":"2022-02-22T07:20:12Z","publisher":"Institute of Science and Technology Austria","year":"2022","citation":{"ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>","apa":"Rzadkowski, W. (2022). <i>Analytic and machine learning approaches to composite quantum impurities</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10759\">https://doi.org/10.15479/at:ista:10759</a>","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","mla":"Rzadkowski, Wojciech. <i>Analytic and Machine Learning Approaches to Composite Quantum Impurities</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10759\">10.15479/at:ista:10759</a>.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022."},"date_updated":"2024-08-07T07:16:53Z","day":"21","doi":"10.15479/at:ista:10759","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data."}],"ddc":["530"],"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","month":"02","language":[{"iso":"eng"}],"type":"dissertation","date_published":"2022-02-21T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"}],"file":[{"access_level":"closed","relation":"source_file","creator":"wrzadkow","file_id":"10785","checksum":"0fc54ad1eaede879c665ac9b53c93e22","file_size":17668233,"date_created":"2022-02-21T13:58:16Z","content_type":"application/zip","file_name":"Rzadkowski_thesis_final_source.zip","date_updated":"2022-02-22T07:20:12Z"},{"access_level":"open_access","relation":"main_file","success":1,"file_id":"10786","creator":"wrzadkow","date_created":"2022-02-21T14:02:54Z","file_size":13307331,"checksum":"22d2d7af37ca31f6b1730c26cac7bced","date_updated":"2022-02-21T14:02:54Z","file_name":"Rzadkowski_thesis_final.pdf","content_type":"application/pdf"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10762","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7956"},{"id":"415","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8644"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public"},{"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","volume":377,"ddc":["570"],"day":"11","doi":"10.1098/rstb.2021.0009","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"citation":{"ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848)."},"year":"2022","date_updated":"2025-05-26T09:05:09Z","external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"isi":1,"publisher":"The Royal Society","article_type":"original","quality_controlled":"1","file_date_updated":"2022-08-02T06:14:32Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-02-21T16:08:10Z","article_processing_charge":"No","publication_status":"published","intvolume":"       377","title":"The response of a metapopulation to a changing environment","scopus_import":"1","_id":"10787","pmid":1,"issue":"1848","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Oluwafunmilola O","last_name":"Olusanya","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":1349672,"checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","date_created":"2022-08-02T06:14:32Z","content_type":"application/pdf","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","date_updated":"2022-08-02T06:14:32Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"11719"}],"status":"public","related_material":{"record":[{"status":"public","id":"14711","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-04-11T00:00:00Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"language":[{"iso":"eng"}],"project":[{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"oa_version":"Published Version","month":"04","has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"ddc":["000"],"day":"08","degree_awarded":"PhD","doi":"10.15479/at:ista:10799","abstract":[{"text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.","lang":"eng"}],"year":"2022","citation":{"mla":"Konstantinov, Nikola H. <i>Robustness and Fairness in Machine Learning</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022.","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","apa":"Konstantinov, N. H. (2022). <i>Robustness and fairness in machine learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>."},"date_updated":"2023-10-17T12:31:54Z","publisher":"Institute of Science and Technology Austria","ec_funded":1,"page":"176","file_date_updated":"2022-03-10T12:11:48Z","date_created":"2022-02-28T13:03:49Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"article_processing_charge":"No","publication_status":"published","title":"Robustness and fairness in machine learning","alternative_title":["ISTA Thesis"],"_id":"10799","author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":4204905,"checksum":"626bc523ae8822d20e635d0e2d95182e","date_created":"2022-03-06T11:42:54Z","content_type":"application/pdf","file_name":"thesis.pdf","date_updated":"2022-03-06T11:42:54Z","relation":"main_file","access_level":"open_access","success":1,"creator":"nkonstan","file_id":"10823"},{"date_created":"2022-03-06T11:42:57Z","file_size":22841103,"checksum":"e2ca2b88350ac8ea1515b948885cbcb1","date_updated":"2022-03-10T12:11:48Z","file_name":"thesis.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"10824","creator":"nkonstan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"8724","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10803"},{"id":"10802","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6590"}]},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-015-2"]},"oa":1,"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","date_published":"2022-03-08T00:00:00Z","keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","month":"03","has_accepted_license":"1"}]