[{"status":"public","ddc":["599","573"],"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12716","file":[{"file_name":"Burnett_Thesis_2023.docx","access_level":"closed","file_size":23029260,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lburnett","relation":"source_file","file_id":"12717","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"creator":"lburnett","file_size":11959869,"content_type":"application/pdf","file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718","relation":"main_file"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"page":"178","citation":{"mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023."},"date_published":"2023-03-10T00:00:00Z","day":"10","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_created":"2023-03-08T15:19:45Z","date_updated":"2023-04-05T10:59:04Z","author":[{"full_name":"Burnett, Laura","first_name":"Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X"}],"file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"supervisor":[{"full_name":"Jösch, Maximilian A","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12716","month":"03","publication_identifier":{"issn":["2663-337X"]}},{"citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria."},"page":"127","date_published":"2023-03-23T00:00:00Z","day":"23","has_accepted_license":"1","article_processing_charge":"No","_id":"12781","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570","572"],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","status":"public","oa_version":"Published Version","file":[{"file_size":6071553,"content_type":"application/pdf","creator":"vkravchu","access_level":"closed","embargo_to":"local","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","checksum":"5ebb6345cb4119f93460c81310265a6d","date_created":"2023-04-19T14:33:41Z","date_updated":"2023-04-19T14:33:41Z","relation":"main_file","embargo":"2024-04-20","file_id":"12852"},{"date_updated":"2023-04-20T07:02:59Z","date_created":"2023-04-19T14:33:52Z","checksum":"c12055c48411d030d2afa51de2166221","file_id":"12853","embargo":"2024-04-20","relation":"source_file","creator":"vkravchu","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19468766,"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","embargo_to":"local","access_level":"closed"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","grant_number":"101020697","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"doi":"10.15479/at:ista:12781","supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"author":[{"first_name":"Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","full_name":"Kravchuk, Vladyslav"}],"related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-08-04T08:54:51Z","date_created":"2023-03-31T12:24:42Z","file_date_updated":"2023-04-20T07:02:59Z","ec_funded":1},{"file_date_updated":"2023-05-24T16:12:59Z","ec_funded":1,"year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","last_name":"Peste"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11458"},{"status":"public","relation":"part_of_dissertation","id":"13053"},{"id":"12299","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-08-04T10:33:27Z","date_created":"2023-05-23T17:07:53Z","month":"05","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"doi":"10.15479/at:ista:13074","degree_awarded":"PhD","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"_id":"13074","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["000"],"status":"public","title":"Efficiency and generalization of sparse neural networks","file":[{"file_id":"13087","relation":"main_file","success":1,"checksum":"6b3354968403cb9d48cc5a83611fb571","date_created":"2023-05-24T16:11:16Z","date_updated":"2023-05-24T16:11:16Z","access_level":"open_access","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","creator":"epeste","file_size":2152072,"content_type":"application/pdf"},{"creator":"epeste","file_size":1658293,"content_type":"application/zip","file_name":"PhD_Thesis_APeste.zip","access_level":"closed","date_updated":"2023-05-24T16:12:59Z","date_created":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_id":"13088","relation":"source_file"}],"oa_version":"Published Version","day":"23","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074"},"page":"147","date_published":"2023-05-23T00:00:00Z"},{"day":"17","article_processing_charge":"No","has_accepted_license":"1","page":"146","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023."},"date_published":"2023-05-17T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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.","lang":"eng"}],"status":"public","title":"Mechanochemical pattern formation across biological scales","ddc":["530"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12964","file":[{"access_level":"closed","file_name":"thesis_boocock.pdf","embargo_to":"open_access","creator":"dboocock","content_type":"application/pdf","file_size":40414730,"embargo":"2024-05-17","file_id":"12988","relation":"main_file","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","date_updated":"2023-05-19T07:04:25Z","date_created":"2023-05-17T13:39:54Z"},{"access_level":"closed","file_name":"thesis_boocock.zip","creator":"dboocock","file_size":34338567,"content_type":"application/zip","file_id":"12989","relation":"source_file","checksum":"581a2313ffeb40fe77e8a122a25a7795","date_created":"2023-05-17T13:39:53Z","date_updated":"2023-05-17T14:35:13Z"}],"oa_version":"Published Version","month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12964","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-05-19T07:04:25Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"year":"2023","date_created":"2023-05-15T14:52:36Z","date_updated":"2023-08-04T11:02:40Z","author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8602"}]}},{"citation":{"chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885"},"page":"82","date_published":"2023-04-28T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"28","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12885","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","status":"public","ddc":["546","541"],"oa_version":"Published Version","file":[{"file_name":"Thesis_Calcabrini.docx","access_level":"closed","creator":"mcalcabr","file_size":99627036,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12887","relation":"source_file","date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z","checksum":"9347b0e09425f56fdcede5d3528404dc"},{"relation":"main_file","file_id":"12888","checksum":"2d188b76621086cd384f0b9264b0a576","success":1,"date_created":"2023-05-02T07:42:45Z","date_updated":"2023-05-02T07:42:45Z","access_level":"open_access","file_name":"Thesis_Calcabrini_pdfa.pdf","content_type":"application/pdf","file_size":8742220,"creator":"mcalcabr"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"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"}],"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:12885","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"month":"04","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"publication_status":"published","related_material":{"record":[{"id":"10806","status":"public","relation":"part_of_dissertation"},{"id":"10042","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12237"},{"status":"public","relation":"part_of_dissertation","id":"9118"},{"status":"public","relation":"part_of_dissertation","id":"10123"}]},"author":[{"orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano","full_name":"Calcabrini, Mariano"}],"date_created":"2023-05-02T07:58:57Z","date_updated":"2023-08-14T07:25:26Z","ec_funded":1,"file_date_updated":"2023-05-02T07:43:18Z"},{"year":"2023","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11470"},{"id":"8308","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11469"},{"relation":"part_of_dissertation","status":"public","id":"12750"}]},"author":[{"full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","first_name":"Pietro"}],"date_updated":"2023-09-20T10:44:12Z","date_created":"2023-03-17T13:30:48Z","ec_funded":1,"file_date_updated":"2023-03-23T16:43:14Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"doi":"10.15479/at:ista:12732","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"publication_identifier":{"issn":["2663-337X"]},"month":"03","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12732","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","ddc":["530"],"status":"public","oa_version":"None","file":[{"file_id":"12753","relation":"source_file","date_created":"2023-03-23T16:42:56Z","date_updated":"2023-03-23T16:42:56Z","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_name":"Thesis_sub_PBrighi.zip","access_level":"closed","creator":"pbrighi","file_size":42167561,"content_type":"application/zip"},{"creator":"pbrighi","content_type":"application/pdf","file_size":13977000,"file_name":"Thesis_PBrighi.pdf","access_level":"open_access","date_updated":"2023-03-23T16:43:14Z","date_created":"2023-03-23T16:43:14Z","success":1,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","file_id":"12754","relation":"main_file"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"citation":{"chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732"},"page":"158","date_published":"2023-03-21T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"21"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12726","ddc":["530"],"title":"Synchronization in collectively moving active matter","status":"public","file":[{"description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","access_level":"closed","creator":"cchlebak","content_type":"application/pdf","file_size":63734746,"file_id":"12745","relation":"main_file","date_updated":"2023-11-24T11:57:46Z","date_created":"2023-03-23T12:49:23Z","checksum":"eba0e19fe57a8c15e7aeab55a845efb7"},{"date_updated":"2023-09-24T22:30:03Z","date_created":"2023-03-23T12:54:34Z","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_id":"12746","relation":"source_file","creator":"cchlebak","file_size":339473651,"content_type":"application/octet-stream","file_name":"Thesis_Riedl_2023_source.rar","embargo_to":"open_access","access_level":"closed"}],"oa_version":"None","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023."},"page":"260","date_published":"2023-03-23T00:00:00Z","day":"23","has_accepted_license":"1","article_processing_charge":"No","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"10791","relation":"part_of_dissertation","status":"public"},{"id":"7932","status":"public","relation":"part_of_dissertation"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"new_edition","id":"14530"}]},"date_updated":"2023-11-30T10:55:13Z","date_created":"2023-03-15T13:22:13Z","file_date_updated":"2023-11-24T11:57:46Z","doi":"10.15479/at:ista:12726","supervisor":[{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2663-337X"]}},{"file_date_updated":"2023-08-18T10:47:55Z","ec_funded":1,"author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma"}],"related_material":{"record":[{"id":"9803","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"12933"},{"relation":"part_of_dissertation","status":"public","id":"6831"},{"id":"14077","status":"public","relation":"part_of_dissertation"}]},"date_created":"2023-08-15T10:20:40Z","date_updated":"2023-12-13T12:15:36Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","month":"08","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:14058","degree_awarded":"PhD","supervisor":[{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"closed","file_name":"Thesis_latex_forpdfa.zip","file_size":10891454,"content_type":"application/zip","creator":"gpuixeus","relation":"source_file","file_id":"14075","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z"},{"file_id":"14079","relation":"main_file","success":1,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-18T10:47:55Z","access_level":"open_access","file_name":"PhDThesis_PuixeuG.pdf","creator":"gpuixeus","content_type":"application/pdf","file_size":19856686}],"oa_version":"Published Version","_id":"14058","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","status":"public","ddc":["576"],"day":"15","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-08-15T00:00:00Z","citation":{"chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058"},"page":"230"},{"month":"09","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"supervisor":[{"full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14280","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2023-10-04T10:28:35Z","ec_funded":1,"date_created":"2023-09-06T10:58:25Z","date_updated":"2024-02-21T12:35:18Z","author":[{"full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp"}],"related_material":{"record":[{"id":"11373","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7387"},{"id":"10934","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","year":"2023","day":"25","has_accepted_license":"1","article_processing_charge":"No","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"date_published":"2023-09-25T00:00:00Z","page":"156","citation":{"apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280."},"abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_id":"14390","relation":"source_file","date_created":"2023-10-04T10:11:53Z","date_updated":"2023-10-04T10:28:35Z","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_name":"PhD Thesis_Philipp Radler_20231004.docx","access_level":"closed","creator":"pradler","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":114932847},{"access_level":"closed","embargo_to":"open_access","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","file_size":37838778,"content_type":"application/pdf","creator":"pradler","relation":"main_file","embargo":"2024-10-04","file_id":"14391","checksum":"3253e099b7126469d941fd9419d68b4f","date_created":"2023-10-04T10:11:21Z","date_updated":"2023-10-04T10:28:35Z"}],"oa_version":"Published Version","status":"public","ddc":["572"],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14280"},{"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"month":"02","language":[{"iso":"eng"}],"supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.15479/at:ista:12491","project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"oa":1,"file_date_updated":"2024-02-08T23:30:04Z","date_updated":"2024-03-25T23:30:05Z","date_created":"2023-02-02T14:50:20Z","related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Zens, Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","first_name":"Bettina","last_name":"Zens"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publication_status":"published","year":"2023","has_accepted_license":"1","article_processing_charge":"No","day":"02","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"date_published":"2023-02-02T00:00:00Z","page":"187","citation":{"mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023."},"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"creator":"bzens","content_type":"application/pdf","file_size":23082464,"access_level":"open_access","file_name":"PhDThesis_BettinaZens_2023_final.pdf","checksum":"069d87f025e0799bf9e3c375664264f2","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z","embargo":"2024-02-07","file_id":"12527","relation":"main_file"},{"file_id":"12528","relation":"source_file","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z","checksum":"8c66ed203495d6e078ed1002a866520c","file_name":"PhDThesis_BettinaZens_2023_final.docx","embargo_to":"open_access","access_level":"closed","creator":"bzens","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":106169509}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","status":"public","ddc":["570"],"_id":"12491","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"page":"201","citation":{"ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470."},"date_published":"2023-01-09T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"09","ddc":["610"],"status":"public","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","_id":"12470","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"20230109_PhD_thesis_JM_final.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":41771714,"embargo":"2023-07-09","file_id":"12471","relation":"main_file","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z","checksum":"1a2306e5f59f52df598e7ecfadf921ac"},{"creator":"cchlebak","file_size":66983464,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"20230109_PhD_thesis_JM_final.docx","embargo_to":"open_access","checksum":"0bebbdee0773443959e1f6ab8caf281f","date_created":"2023-01-31T15:11:51Z","date_updated":"2023-07-10T22:30:04Z","file_id":"12472","relation":"source_file"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"supervisor":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"}],"doi":"10.15479/at:ista:12470","publication_identifier":{"isbn":[" 978-3-99078-026-8"],"issn":["2663-337X"]},"month":"01","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","date_updated":"2023-08-31T12:26:58Z","date_created":"2023-01-31T15:10:53Z","related_material":{"record":[{"id":"11943","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"11950"}]},"author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","last_name":"Michalska"}],"ec_funded":1,"file_date_updated":"2023-07-27T22:30:54Z"},{"author":[{"full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14591"},{"status":"public","relation":"part_of_dissertation","id":"9887"},{"id":"8139","status":"public","relation":"part_of_dissertation"}]},"date_created":"2023-11-10T09:10:06Z","date_updated":"2024-03-28T23:30:46Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-11-23T13:10:55Z","ec_funded":1,"doi":"10.15479/at:ista:14510","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"month":"11","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"file":[{"date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","relation":"source_file","creator":"ngnyliuk","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","access_level":"closed"},{"date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-20T09:23:11Z","checksum":"bfc96d47fc4e7e857dd71656097214a4","embargo":"2024-11-23","file_id":"14568","relation":"main_file","creator":"ngnyliuk","file_size":24871844,"content_type":"application/pdf","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","access_level":"closed"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14510","ddc":["570"],"status":"public","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-11-10T00:00:00Z","citation":{"mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023."},"page":"180","day":"10","article_processing_charge":"No","has_accepted_license":"1","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"]},{"page":"180","citation":{"chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897"},"date_published":"2023-05-05T00:00:00Z","day":"05","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["516","004","518","531"],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","_id":"12897","oa_version":"Published Version","file":[{"date_created":"2023-05-11T10:43:20Z","date_updated":"2023-12-08T23:30:04Z","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","relation":"main_file","file_id":"12942","embargo":"2023-12-07","file_size":50714445,"content_type":"application/pdf","creator":"chafner","file_name":"thesis-hafner-2023may11-a2b.pdf","access_level":"open_access"},{"date_created":"2023-05-11T10:43:44Z","date_updated":"2023-12-08T23:30:04Z","checksum":"a6b51334be2b81672357b1549afab40c","file_id":"12943","relation":"source_file","creator":"chafner","file_size":265319,"content_type":"application/pdf","file_name":"thesis-release-form.pdf","embargo_to":"open_access","access_level":"closed"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"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.","lang":"eng"}],"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa":1,"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12897","month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-031-2"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"year":"2023","date_created":"2023-05-05T10:40:14Z","date_updated":"2024-01-29T10:47:51Z","author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9817"},{"relation":"part_of_dissertation","status":"public","id":"7117"},{"id":"13188","status":"public","relation":"dissertation_contains"}]},"file_date_updated":"2023-12-08T23:30:04Z","ec_funded":1},{"citation":{"ama":"Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072","ieee":"A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.","apa":"Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072","ista":"Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.","short":"A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.","mla":"Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.","chicago":"Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072."},"page":"208","date_published":"2022-09-08T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"08","_id":"12072","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Existence and density problems in Diophantine geometry: From norm forms to Campana points","status":"public","ddc":["512"],"file":[{"success":1,"checksum":"bf073344320e05d92c224786cec2e92d","date_created":"2022-09-08T21:50:34Z","date_updated":"2022-09-08T21:50:34Z","file_id":"12073","relation":"main_file","creator":"ashute","content_type":"application/pdf","file_size":1907386,"access_level":"open_access","file_name":"Thesis_final_draft.pdf"},{"creator":"ashute","file_size":495393,"content_type":"application/octet-stream","access_level":"closed","file_name":"athesis.tex","checksum":"b054ac6baa09f70e8235403a4abbed80","date_created":"2022-09-08T21:50:42Z","date_updated":"2022-09-12T11:24:21Z","file_id":"12074","relation":"source_file"},{"checksum":"0a31e905f1cff5eb8110978cc90e1e79","date_created":"2022-09-09T12:05:00Z","date_updated":"2022-09-12T11:24:21Z","relation":"source_file","file_id":"12078","content_type":"application/x-zip-compressed","file_size":944534,"creator":"ashute","access_level":"closed","file_name":"qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. "}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.15479/at:ista:12072","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","full_name":"Browning, Timothy D"}],"publication_identifier":{"isbn":["978-3-99078-023-7"],"issn":["2663-337X"]},"month":"09","acknowledgement":"I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385.","year":"2022","department":[{"_id":"GradSch"},{"_id":"TiBr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"12076","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12077"}]},"author":[{"first_name":"Alec L","last_name":"Shute","id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810","full_name":"Shute, Alec L"}],"date_created":"2022-09-08T21:53:03Z","date_updated":"2023-02-21T16:37:35Z","ec_funded":1,"file_date_updated":"2022-09-12T11:24:21Z"},{"publisher":"Institute of Science and Technology","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"publication_status":"published","year":"2022","date_updated":"2023-06-22T09:56:36Z","date_created":"2022-08-10T15:51:19Z","author":[{"full_name":"Wild, Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","last_name":"Wild","first_name":"Pascal"}],"ec_funded":1,"file_date_updated":"2022-08-11T16:09:19Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:11777","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"month":"08","title":"High-dimensional expansion and crossing numbers of simplicial complexes","ddc":["500","516","514"],"status":"public","_id":"11777","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_id":"11780","relation":"supplementary_material","date_updated":"2022-08-10T15:34:04Z","date_created":"2022-08-10T15:34:04Z","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","file_name":"flags.py","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","access_level":"open_access","creator":"pwild","content_type":"text/x-python","file_size":16828},{"file_id":"11781","relation":"supplementary_material","date_created":"2022-08-10T15:34:10Z","date_updated":"2022-08-10T15:34:10Z","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_name":"lowerbound.cpp","description":"Code for proof of Lemma 8.20 in Thesis","access_level":"open_access","creator":"pwild","file_size":12226,"content_type":"text/x-c++src"},{"file_size":3240,"content_type":"text/x-python","creator":"pwild","description":"Code for proof of Proposition 7.9 in Thesis","file_name":"upperbound.py","access_level":"open_access","date_created":"2022-08-10T15:34:17Z","date_updated":"2022-08-10T15:34:17Z","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","relation":"supplementary_material","file_id":"11782"},{"file_id":"11809","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","relation":"main_file","date_updated":"2022-08-11T16:08:33Z","date_created":"2022-08-11T16:08:33Z","checksum":"4e96575b10cbe4e0d0db2045b2847774","file_name":"finalthesisPascalWildPDFA.pdf","access_level":"open_access","creator":"pwild","content_type":"application/pdf","file_size":5086282},{"file_name":"ThesisSubmission.zip","access_level":"closed","file_size":18150068,"content_type":"application/zip","creator":"pwild","relation":"source_file","file_id":"11810","date_updated":"2022-08-11T16:09:19Z","date_created":"2022-08-11T16:09:19Z","checksum":"92d94842a1fb6dca5808448137573b2e"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.","lang":"eng"}],"page":"170","citation":{"ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","apa":"Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777.","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","mla":"Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777."},"date_published":"2022-08-11T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"11"},{"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","file_name":"LenkaPhD_Official_PDFA.pdf","content_type":"application/pdf","file_size":11906472,"creator":"cchlebak","relation":"main_file","file_id":"11129","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","date_updated":"2022-04-07T08:11:34Z","date_created":"2022-04-07T08:11:34Z"},{"content_type":"application/x-zip-compressed","file_size":23036766,"creator":"cchlebak","access_level":"closed","file_name":"LenkaPhD Official_source.zip","checksum":"99d67040432fd07a225643a212ee8588","date_created":"2022-04-07T08:11:51Z","date_updated":"2022-04-07T08:11:51Z","relation":"source_file","file_id":"11130"}],"oa_version":"Published Version","_id":"11128","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["576","582"],"title":"Genetic basis of flower colour as a model for adaptive evolution","status":"public","day":"06","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-04-06T00:00:00Z","citation":{"chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128"},"page":"112","file_date_updated":"2022-04-07T08:11:51Z","author":[{"full_name":"Matejovicova, Lenka","first_name":"Lenka","last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-06-23T06:26:41Z","date_created":"2022-04-07T08:19:54Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","month":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"doi":"10.15479/at:ista:11128","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"year":"2022","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11995"}]},"author":[{"full_name":"Schulz, Rouven","first_name":"Rouven","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5297-733X"}],"date_updated":"2023-08-03T13:02:26Z","date_created":"2022-08-23T11:33:11Z","file_date_updated":"2022-08-25T09:33:31Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:11945","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"supervisor":[{"last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"08","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11945","status":"public","title":"Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"11970","relation":"main_file","success":1,"checksum":"61b1b666a210ff7cdd0e95ea75207a13","date_created":"2022-08-25T08:59:57Z","date_updated":"2022-08-25T08:59:57Z","access_level":"open_access","file_name":"Thesis_Rouven_Schulz_2022_final.pdf","creator":"rschulz","content_type":"application/pdf","file_size":28079331},{"checksum":"2b8f95ea1c134dbdb927b41b1dbeeeb5","date_created":"2022-08-25T09:00:11Z","date_updated":"2022-08-25T09:33:31Z","relation":"source_file","file_id":"11971","file_size":27226963,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rschulz","access_level":"closed","file_name":"Thesis_Rouven_Schulz_2022_final.docx"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level."}],"citation":{"short":"R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022.","mla":"Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945.","chicago":"Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945.","ama":"Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945","ieee":"R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022.","apa":"Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945","ista":"Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria."},"page":"133","date_published":"2022-08-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23"},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"year":"2022","date_updated":"2023-08-07T13:32:09Z","date_created":"2023-01-26T10:00:42Z","author":[{"id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928","first_name":"Morris","last_name":"Brooks","full_name":"Brooks, Morris"}],"related_material":{"record":[{"id":"9005","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2023-01-26T10:02:42Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"supervisor":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12390","month":"12","publication_identifier":{"issn":["2663-337X"]},"status":"public","ddc":["500"],"title":"Translation-invariant quantum systems with effectively broken symmetry","_id":"12390","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_size":3095225,"content_type":"application/pdf","creator":"cchlebak","file_name":"Brooks_Thesis.pdf","access_level":"open_access","date_created":"2023-01-26T10:02:34Z","date_updated":"2023-01-26T10:02:34Z","checksum":"b31460e937f33b557abb40ebef02b567","success":1,"relation":"main_file","file_id":"12391"},{"date_updated":"2023-01-26T10:02:42Z","date_created":"2023-01-26T10:02:42Z","checksum":"9751869fa5e7981588ad4228f4fd4bd6","relation":"source_file","file_id":"12392","content_type":"application/octet-stream","file_size":809842,"creator":"cchlebak","file_name":"Brooks_Thesis.tex","access_level":"closed"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n","lang":"eng"}],"page":"196","citation":{"chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390.","mla":"Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022.","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","apa":"Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390"},"date_published":"2022-12-15T00:00:00Z","day":"15","has_accepted_license":"1","article_processing_charge":"No"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"_id":"12368","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Remodeling of E-cadherin-mediated contacts via cortical flows","status":"public","file":[{"relation":"main_file","file_id":"12369","date_updated":"2023-01-25T10:52:46Z","date_created":"2023-01-25T10:52:46Z","checksum":"e54a3e69b83ebf166544164afd25608e","success":1,"file_name":"THESIS_FINAL_FArslan_pdfa.pdf","access_level":"open_access","content_type":"application/pdf","file_size":14581024,"creator":"cchlebak"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"29","citation":{"chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153.","mla":"Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153.","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical Flows, Institute of Science and Technology Austria, 2022.","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical flows,” Institute of Science and Technology Austria, 2022.","apa":"Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical flows. 2022. doi:10.15479/at:ista:12153"},"page":"113","date_published":"2022-09-29T00:00:00Z","ec_funded":1,"file_date_updated":"2023-01-25T10:52:46Z","year":"2022","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"9350","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Arslan, Feyza N","last_name":"Arslan","first_name":"Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-08T13:14:10Z","date_created":"2023-01-25T10:43:24Z","publication_identifier":{"isbn":[" 978-3-99078-025-1 "],"issn":["2663-337X"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"doi":"10.15479/at:ista:12153","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}]},{"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"year":"2022","date_created":"2022-06-30T12:15:03Z","date_updated":"2023-09-07T13:43:52Z","author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10564"},{"relation":"part_of_dissertation","status":"public","id":"8705"}]},"file_date_updated":"2022-07-05T08:17:12Z","ec_funded":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11473","month":"07","publication_identifier":{"issn":["2663-337X"]},"ddc":["515","539"],"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"11473","oa_version":"Published Version","file":[{"file_name":"thes1_no_isbn_2_1b.pdf","access_level":"open_access","creator":"kmysliwy","content_type":"application/pdf","file_size":1830973,"file_id":"11486","relation":"main_file","date_created":"2022-07-05T08:12:56Z","date_updated":"2022-07-05T08:12:56Z","success":1,"checksum":"7970714a20a6052f75fb27a6c3e9976e"},{"relation":"source_file","file_id":"11487","checksum":"647a2011fdf56277096c9350fefe1097","date_updated":"2022-07-05T08:17:12Z","date_created":"2022-07-05T08:15:52Z","access_level":"closed","file_name":"thes_source.zip","file_size":5831060,"content_type":"application/zip","creator":"kmysliwy"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n","lang":"eng"}],"page":"138","citation":{"chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11473.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","mla":"Mysliwy, Krzysztof. Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11473.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","apa":"Mysliwy, K. (2022). Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11473","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:10.15479/at:ista:11473"},"date_published":"2022-07-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10823","date_updated":"2022-03-06T11:42:54Z","date_created":"2022-03-06T11:42:54Z","checksum":"626bc523ae8822d20e635d0e2d95182e","success":1,"file_name":"thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4204905,"creator":"nkonstan"},{"date_created":"2022-03-06T11:42:57Z","date_updated":"2022-03-10T12:11:48Z","checksum":"e2ca2b88350ac8ea1515b948885cbcb1","file_id":"10824","relation":"source_file","creator":"nkonstan","content_type":"application/x-zip-compressed","file_size":22841103,"file_name":"thesis.zip","access_level":"closed"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10799","title":"Robustness and fairness in machine learning","ddc":["000"],"status":"public","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"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2022-03-08T00:00:00Z","citation":{"mla":"Konstantinov, Nikola H. Robustness and Fairness in Machine Learning. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10799.","short":"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. https://doi.org/10.15479/at:ista:10799.","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:10.15479/at:ista:10799","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","apa":"Konstantinov, N. H. (2022). Robustness and fairness in machine learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10799"},"page":"176","has_accepted_license":"1","article_processing_charge":"No","day":"08","keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"related_material":{"record":[{"id":"8724","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10803"},{"id":"10802","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6590"}]},"author":[{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H"}],"date_created":"2022-02-28T13:03:49Z","date_updated":"2023-10-17T12:31:54Z","year":"2022","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2022-03-10T12:11:48Z","doi":"10.15479/at:ista:10799","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"degree_awarded":"PhD","oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"month":"03"},{"month":"07","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"oa":1,"supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11626","file_date_updated":"2022-07-25T11:48:45Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"year":"2022","date_created":"2022-07-20T11:21:53Z","date_updated":"2023-11-07T08:20:13Z","author":[{"orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","full_name":"Gallei, Michelle C"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8931"},{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7142"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"id":"8138","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"id":"10411","status":"public","relation":"part_of_dissertation"}]},"day":"20","has_accepted_license":"1","article_processing_charge":"No","page":"248","citation":{"chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626"},"date_published":"2022-07-20T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"ddc":["575"],"status":"public","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11626","oa_version":"Published Version","file":[{"date_updated":"2022-07-25T09:08:47Z","date_created":"2022-07-25T09:08:47Z","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","relation":"main_file","file_id":"11645","file_size":9730864,"content_type":"application/pdf","creator":"mgallei","file_name":"Thesis_Gallei.pdf","access_level":"open_access"},{"date_created":"2022-07-25T09:09:09Z","date_updated":"2022-07-25T09:39:58Z","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","file_id":"11646","relation":"source_file","creator":"mgallei","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19560720,"file_name":"Thesis_Gallei_source.docx","access_level":"closed"},{"description":"This is the print version of the thesis including the full appendix","file_name":"Thesis_Gallei_to_print.pdf","access_level":"closed","file_size":24542837,"content_type":"application/pdf","creator":"mgallei","relation":"source_file","file_id":"11647","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:32Z","checksum":"3994f7f20058941b5bb8a16886b21e71"},{"access_level":"open_access","file_name":"Thesis_Gallei_Appendix.pdf","creator":"mgallei","file_size":15435966,"content_type":"application/pdf","file_id":"11650","relation":"main_file","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","date_updated":"2022-07-25T11:48:45Z","date_created":"2022-07-25T11:48:45Z"}]},{"doi":"10.15479/at:ista:12103","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"oa":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"month":"09","related_material":{"record":[{"id":"11736","relation":"part_of_dissertation","status":"public"},{"id":"9818","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8385"}]},"author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl"}],"date_created":"2023-01-24T10:49:46Z","date_updated":"2024-02-28T12:57:46Z","year":"2022","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","ec_funded":1,"file_date_updated":"2023-02-02T09:39:25Z","date_published":"2022-09-22T00:00:00Z","citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","apa":"Sperl, G. (2022). Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12103","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:10.15479/at:ista:12103","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12103.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12103."},"page":"138","has_accepted_license":"1","article_processing_charge":"No","day":"22","file":[{"file_id":"12371","title":"Thesis","relation":"main_file","checksum":"083722acbb8115e52e3b0fdec6226769","date_updated":"2023-02-02T09:29:57Z","date_created":"2023-01-25T12:04:41Z","access_level":"open_access","description":"This is the main PDF file of the thesis. File size: 105 MB","file_name":"thesis_gsperl.pdf","creator":"cchlebak","file_size":104497530,"content_type":"application/pdf"},{"access_level":"open_access","file_name":"thesis_gsperl_compressed.pdf","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","creator":"cchlebak","file_size":23183710,"content_type":"application/pdf","file_id":"12483","title":"Thesis (compressed 23MB)","relation":"main_file","checksum":"511f82025e5fcb70bff4731d6896ca07","date_created":"2023-02-02T09:33:37Z","date_updated":"2023-02-02T09:33:37Z"},{"access_level":"open_access","file_name":"thesis-source.zip","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":98382247,"file_id":"12484","relation":"source_file","checksum":"ed4cb85225eedff761c25bddfc37a2ed","date_updated":"2023-02-02T09:39:25Z","date_created":"2023-02-02T09:39:25Z"}],"oa_version":"Published Version","_id":"12358","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","ddc":["000","620"],"status":"public","abstract":[{"lang":"eng","text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"month":"02","publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10759","file_date_updated":"2022-02-22T07:20:12Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"year":"2022","date_created":"2022-02-16T13:27:37Z","date_updated":"2024-02-28T13:01:59Z","author":[{"orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","first_name":"Wojciech","full_name":"Rzadkowski, Wojciech"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10762"},{"id":"8644","status":"public","relation":"part_of_dissertation"},{"id":"7956","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"415"}]},"day":"21","article_processing_charge":"No","has_accepted_license":"1","page":"120","citation":{"apa":"Rzadkowski, W. (2022). Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10759","ieee":"W. Rzadkowski, “Analytic and machine learning approaches to composite quantum impurities,” Institute of Science and Technology Austria, 2022.","ista":"Rzadkowski W. 2022. Analytic and machine learning approaches to composite quantum impurities. Institute of Science and Technology Austria.","ama":"Rzadkowski W. Analytic and machine learning approaches to composite quantum impurities. 2022. doi:10.15479/at:ista:10759","chicago":"Rzadkowski, Wojciech. “Analytic and Machine Learning Approaches to Composite Quantum Impurities.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:10759.","short":"W. Rzadkowski, Analytic and Machine Learning Approaches to Composite Quantum Impurities, Institute of Science and Technology Austria, 2022.","mla":"Rzadkowski, Wojciech. Analytic and Machine Learning Approaches to Composite Quantum Impurities. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:10759."},"date_published":"2022-02-21T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","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."}],"title":"Analytic and machine learning approaches to composite quantum impurities","status":"public","ddc":["530"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10759","file":[{"access_level":"closed","file_name":"Rzadkowski_thesis_final_source.zip","creator":"wrzadkow","content_type":"application/zip","file_size":17668233,"file_id":"10785","relation":"source_file","checksum":"0fc54ad1eaede879c665ac9b53c93e22","date_updated":"2022-02-22T07:20:12Z","date_created":"2022-02-21T13:58:16Z"},{"success":1,"checksum":"22d2d7af37ca31f6b1730c26cac7bced","date_updated":"2022-02-21T14:02:54Z","date_created":"2022-02-21T14:02:54Z","file_id":"10786","relation":"main_file","creator":"wrzadkow","file_size":13307331,"content_type":"application/pdf","access_level":"open_access","file_name":"Rzadkowski_thesis_final.pdf"}],"oa_version":"Published Version"},{"project":[{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","grant_number":"708497"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11196","month":"04","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","year":"2022","date_updated":"2023-08-18T06:31:52Z","date_created":"2022-04-20T09:47:12Z","author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Olena","full_name":"Kim, Olena"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11222"},{"status":"public","relation":"part_of_dissertation","id":"7473"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2023-04-20T22:30:03Z","ec_funded":1,"page":"132","citation":{"ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:10.15479/at:ista:11196","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","apa":"Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196","mla":"Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196."},"date_published":"2022-04-20T00:00:00Z","day":"20","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","status":"public","_id":"11196","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"checksum":"1616a8bf6f13a57c892dac873dcd0936","date_updated":"2023-04-20T22:30:03Z","date_created":"2022-04-20T14:21:56Z","file_id":"11220","embargo":"2023-04-19","relation":"main_file","creator":"okim","file_size":21273537,"content_type":"application/pdf","access_level":"open_access","file_name":"Olena_KIM_thesis_final.pdf"},{"creator":"okim","content_type":"application/x-zip-compressed","file_size":59248569,"file_name":"KIM_thesis_final.zip","embargo_to":"open_access","access_level":"closed","date_updated":"2023-04-20T22:30:03Z","date_created":"2022-04-20T14:22:56Z","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","file_id":"11221","relation":"source_file"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n","lang":"eng"}]},{"oa":1,"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"doi":"10.15479/AT:ISTA:10727","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publication_identifier":{"issn":["2663-337X"]},"month":"02","year":"2022","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina"}],"date_created":"2022-02-04T15:45:12Z","date_updated":"2023-09-07T13:43:23Z","ec_funded":1,"file_date_updated":"2023-02-04T23:30:03Z","citation":{"ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:10.15479/AT:ISTA:10727","apa":"Metzler, S. (2022). Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10727","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","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. Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10727.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10727."},"date_published":"2022-02-07T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"07","_id":"10727","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Pathogen-mediated sexual selection and immunization in ant colonies","status":"public","ddc":["570"],"file":[{"access_level":"closed","file_name":"Thesis_Sina_Metzler.docx","embargo_to":"open_access","creator":"smetzler","file_size":6757886,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10728","relation":"source_file","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","date_updated":"2023-02-03T23:30:03Z","date_created":"2022-02-04T15:36:12Z"},{"file_name":"Thesis_Sina_Metzler_A2.pdf","access_level":"open_access","creator":"smetzler","content_type":"application/pdf","file_size":6314921,"embargo":"2023-02-02","file_id":"10730","relation":"main_file","date_updated":"2023-02-03T23:30:03Z","date_created":"2022-02-04T15:36:43Z","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027"},{"creator":"smetzler","file_size":6882557,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Sina_Metzler_print.pdf","checksum":"dedd14b7be7a75d63018dbfc68dd8113","date_updated":"2023-02-04T23:30:03Z","date_created":"2022-02-07T10:35:02Z","file_id":"10742","embargo":"2023-02-02","relation":"main_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"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.","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","file_size":11113608,"content_type":"application/pdf","creator":"cartner","relation":"main_file","file_id":"11907","embargo":"2023-09-08","checksum":"a2c2fdc28002538840490bfa6a08b2cb","date_created":"2022-08-17T12:08:49Z","date_updated":"2023-09-09T22:30:03Z"},{"file_id":"11908","relation":"source_file","checksum":"66b461c074b815fbe63481b3f46a9f43","date_created":"2022-08-17T12:08:59Z","date_updated":"2023-09-09T22:30:03Z","access_level":"closed","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","embargo_to":"open_access","creator":"cartner","content_type":"application/octet-stream","file_size":19097730}],"oa_version":"Published Version","_id":"11879","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","ddc":["580"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"17","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"date_published":"2022-08-17T00:00:00Z","citation":{"ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:10.15479/at:ista:11879","apa":"Artner, C. (2022). Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11879","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","mla":"Artner, Christina. Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11879.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11879."},"page":"128","file_date_updated":"2023-09-09T22:30:03Z","author":[{"full_name":"Artner, Christina","first_name":"Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-09T22:30:04Z","date_created":"2022-08-17T07:58:53Z","year":"2022","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-022-0"]},"month":"08","doi":"10.15479/at:ista:11879","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"degree_awarded":"PhD","oa":1,"project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}]},{"day":"16","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-05-16T00:00:00Z","citation":{"ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","apa":"Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","mla":"Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393."},"page":"108","abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"access_level":"closed","embargo_to":"open_access","file_name":"MJ thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":56427603,"creator":"cchlebak","relation":"source_file","file_id":"11395","checksum":"8fc695d88020d70d231dad0e9f10b138","date_updated":"2023-05-17T22:30:03Z","date_created":"2022-05-17T09:08:06Z"},{"file_size":4351981,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"MJ_thesis_PDFA.pdf","checksum":"c1dd20a1aece521b3500607b00e463d6","date_created":"2022-05-17T12:09:25Z","date_updated":"2023-05-17T22:30:03Z","relation":"main_file","embargo":"2023-05-16","file_id":"11397"}],"_id":"11393","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","status":"public","ddc":["570"],"month":"05","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11393","acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2023-05-17T22:30:03Z","author":[{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo","last_name":"Jevtic","full_name":"Jevtic, Marijo"}],"related_material":{"record":[{"id":"7391","status":"public","relation":"part_of_dissertation"}]},"date_created":"2022-05-17T08:57:41Z","date_updated":"2023-09-07T14:53:44Z","year":"2022","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}]},{"oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":56076868,"access_level":"open_access","file_name":"Final_Thesis_ES_Redchenko.pdf","checksum":"39eabb1e006b41335f17f3b29af09648","date_created":"2023-01-25T09:41:49Z","date_updated":"2023-01-26T23:30:44Z","embargo":"2022-12-28","file_id":"12367","relation":"main_file"}],"_id":"12366","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Controllable states of superconducting Qubit ensembles","ddc":["530"],"abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2022-09-26T00:00:00Z","citation":{"mla":"Redchenko, Elena. Controllable States of Superconducting Qubit Ensembles. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12132.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12132.","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:10.15479/at:ista:12132","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","apa":"Redchenko, E. (2022). Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12132"},"page":"168","day":"26","has_accepted_license":"1","article_processing_charge":"No","author":[{"id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena"}],"date_created":"2023-01-25T09:17:02Z","date_updated":"2023-05-26T09:29:07Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-01-26T23:30:44Z","ec_funded":1,"doi":"10.15479/at:ista:12132","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"}],"month":"09","publication_identifier":{"isbn":["978-3-99078-024-4"],"issn":["2663-337X"]}},{"month":"08","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:11932","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"file_date_updated":"2023-06-20T22:30:04Z","ec_funded":1,"author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele"}],"related_material":{"record":[{"id":"10077","status":"public","relation":"part_of_dissertation"},{"id":"6194","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-05T12:02:14Z","date_created":"2022-08-19T08:52:30Z","year":"2022","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","day":"19","article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-08-19T00:00:00Z","citation":{"short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","mla":"Nardin, Michele. On the Encoding, Transfer, and Consolidation of Spatial Memories. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11932.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11932.","ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:10.15479/at:ista:11932","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","apa":"Nardin, M. (2022). On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11932","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria."},"page":"136","abstract":[{"text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","embargo_to":"open_access","access_level":"closed","creator":"mnardin","content_type":"application/zip","file_size":13515457,"file_id":"11935","relation":"source_file","date_created":"2022-08-19T16:31:34Z","date_updated":"2023-06-20T22:30:04Z","checksum":"2dbb70c74aaa3b64c1f463e943baf09c"},{"embargo":"2023-06-19","file_id":"11941","relation":"main_file","checksum":"0ec94035ea35a47a9f589ed168e60b48","date_updated":"2023-06-20T22:30:04Z","date_created":"2022-08-22T09:43:50Z","access_level":"open_access","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","creator":"mnardin","file_size":9906458,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11932","status":"public","ddc":["573"],"title":"On the encoding, transfer, and consolidation of spatial memories"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"status":"public","title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","ddc":["570"],"_id":"12378","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Gloria_Colombo_Thesis.docx","embargo_to":"open_access","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23890382,"file_id":"12379","relation":"source_file","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","date_updated":"2023-04-12T22:30:03Z","date_created":"2023-01-25T14:31:32Z"},{"access_level":"open_access","file_name":"Gloria_Colombo_Thesis.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":13802421,"file_id":"12380","embargo":"2023-04-11","relation":"main_file","checksum":"8af4319c18b516e8758e9a6cb02b103b","date_created":"2023-01-25T14:31:36Z","date_updated":"2023-04-12T22:30:03Z"}],"article_processing_charge":"No","has_accepted_license":"1","day":"11","page":"142","citation":{"ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","apa":"Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022.","mla":"Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378.","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378."},"date_published":"2022-11-11T00:00:00Z","ec_funded":1,"file_date_updated":"2023-04-12T22:30:03Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"publication_status":"published","year":"2022","date_created":"2023-01-25T14:27:43Z","date_updated":"2023-08-04T09:40:37Z","related_material":{"record":[{"id":"12244","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","first_name":"Gloria","full_name":"Colombo, Gloria"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"supervisor":[{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"doi":"10.15479/at:ista:12378"},{"month":"12","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/at:ista:12401","degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"language":[{"iso":"eng"}],"file_date_updated":"2023-12-21T23:30:03Z","year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","full_name":"Tasciyan, Saren"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"679"},{"relation":"part_of_dissertation","status":"public","id":"10703"},{"id":"9429","relation":"part_of_dissertation","status":"public"},{"id":"7885","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-12-21T23:30:04Z","date_created":"2023-01-26T11:55:16Z","day":"22","article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","apa":"Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401.","mla":"Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022."},"page":"105","date_published":"2022-12-22T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"_id":"12401","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Role of microenvironment heterogeneity in cancer cell invasion","ddc":["610"],"oa_version":"Published Version","file":[{"date_created":"2023-01-26T11:58:14Z","date_updated":"2023-12-21T23:30:03Z","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","relation":"main_file","file_id":"12402","embargo":"2023-12-20","file_size":42059787,"content_type":"application/pdf","creator":"cchlebak","file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","access_level":"open_access"},{"content_type":"application/x-zip-compressed","file_size":261256696,"creator":"cchlebak","embargo_to":"open_access","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","access_level":"closed","date_updated":"2023-12-21T23:30:03Z","date_created":"2023-01-26T12:00:10Z","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","relation":"source_file","file_id":"12403"}]},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":8820951,"creator":"cchlebak","file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","access_level":"open_access","date_created":"2022-04-20T09:03:57Z","date_updated":"2023-04-21T22:30:03Z","checksum":"999ab16884c4522486136ebc5ae8dbff","relation":"main_file","file_id":"11195","embargo":"2023-04-20"},{"relation":"source_file","file_id":"11329","date_created":"2022-04-22T12:41:00Z","date_updated":"2023-04-21T22:30:03Z","checksum":"fd92b1e38d53bdf8b458213882d41383","embargo_to":"open_access","file_name":"Thesis_Stephanie_Wachner_20200414.zip","access_level":"closed","file_size":65864612,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"status":"public","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","ddc":["570"],"_id":"11193","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2022-04-20T00:00:00Z","page":"170","citation":{"mla":"Wachner, Stephanie. Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11193.","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11193.","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:10.15479/at:ista:11193","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","apa":"Wachner, S. (2022). Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11193","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022."},"day":"20","has_accepted_license":"1","article_processing_charge":"No","date_updated":"2023-09-19T10:15:54Z","date_created":"2022-04-20T08:59:07Z","author":[{"full_name":"Wachner, Stephanie","last_name":"Wachner","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10614"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"year":"2022","file_date_updated":"2023-04-21T22:30:03Z","acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:11193","project":[{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04","publication_identifier":{"issn":["2663-337X"]}},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence."}],"_id":"12364","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","status":"public","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":20457465,"access_level":"open_access","file_name":"220923_Thesis_CDotter_Final.pdf","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","date_updated":"2023-09-20T22:30:03Z","date_created":"2023-01-24T13:15:45Z","embargo":"2023-09-19","file_id":"12365","relation":"main_file"},{"relation":"source_file","file_id":"12482","checksum":"ad01bb20da163be6893b7af832e58419","date_updated":"2023-09-20T22:30:03Z","date_created":"2023-02-02T09:15:35Z","access_level":"closed","embargo_to":"open_access","file_name":"latex_source_CDotter_Thesis_2022.zip","file_size":22433512,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"oa_version":"Published Version","day":"19","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12094.","mla":"Dotter, Christoph. Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12094.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","apa":"Dotter, C. (2022). Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12094","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:10.15479/at:ista:12094"},"page":"152","date_published":"2022-09-19T00:00:00Z","file_date_updated":"2023-09-20T22:30:03Z","ec_funded":1,"year":"2022","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","full_name":"Dotter, Christoph"}],"related_material":{"record":[{"id":"3","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11160"}]},"date_created":"2023-01-24T13:09:57Z","date_updated":"2023-11-16T13:10:22Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299"},{"grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"grant_number":"I04205","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"doi":"10.15479/at:ista:12094","supervisor":[{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}]},{"degree_awarded":"PhD","supervisor":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9056","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","publication_identifier":{"issn":["2663-337X"]},"date_created":"2021-02-02T14:11:06Z","date_updated":"2023-09-07T13:29:01Z","author":[{"last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"}],"related_material":{"record":[{"id":"187","status":"public","relation":"part_of_dissertation"},{"id":"8703","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"year":"2021","file_date_updated":"2021-02-03T10:37:28Z","place":"Klosterneuburg","date_published":"2021-02-01T00:00:00Z","page":"134","citation":{"ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","apa":"Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","mla":"Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"content_type":"application/zip","file_size":13446994,"creator":"patrickd","access_level":"closed","file_name":"thesis_source.zip","checksum":"bcf27986147cab0533b6abadd74e7629","date_created":"2021-02-02T14:09:25Z","date_updated":"2021-02-03T10:37:28Z","relation":"source_file","file_id":"9063"},{"relation":"main_file","file_id":"9064","checksum":"9cc8af266579a464385bbe2aff6af606","success":1,"date_updated":"2021-02-02T14:09:18Z","date_created":"2021-02-02T14:09:18Z","access_level":"open_access","file_name":"thesis_pdfA2b.pdf","file_size":5210329,"content_type":"application/pdf","creator":"patrickd"}],"ddc":["006","514","516"],"status":"public","title":"Multi-cover persistence and Delaunay mosaics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9056","abstract":[{"text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"file_date_updated":"2021-01-25T14:19:10Z","ec_funded":1,"year":"2021","acknowledgement":"I gratefully acknowledge the financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and my advisor’s ERC Advanced Grant No. 338804.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992"}],"date_updated":"2023-09-07T13:29:32Z","date_created":"2021-01-21T18:16:54Z","month":"01","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:9022","degree_awarded":"PhD","supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.\r\nIn the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time\r\n(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.\r\nIn the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result\r\nimproves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9022","ddc":["510"],"status":"public","title":"Fluctuations in the spectrum of random matrices","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9043","checksum":"5a93658a5f19478372523ee232887e2b","success":1,"date_created":"2021-01-25T14:19:03Z","date_updated":"2021-01-25T14:19:03Z","access_level":"open_access","file_name":"thesis.pdf","content_type":"application/pdf","file_size":4127796,"creator":"gcipollo"},{"file_name":"Thesis_files.zip","access_level":"closed","file_size":12775206,"content_type":"application/zip","creator":"gcipollo","relation":"source_file","file_id":"9044","date_updated":"2021-01-25T14:19:10Z","date_created":"2021-01-25T14:19:10Z","checksum":"e8270eddfe6a988e92a53c88d1d19b8c"}],"day":"25","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Cipolloni G. Fluctuations in the spectrum of random matrices. 2021. doi:10.15479/AT:ISTA:9022","ista":"Cipolloni G. 2021. Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria.","apa":"Cipolloni, G. (2021). Fluctuations in the spectrum of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9022","ieee":"G. Cipolloni, “Fluctuations in the spectrum of random matrices,” Institute of Science and Technology Austria, 2021.","mla":"Cipolloni, Giorgio. Fluctuations in the Spectrum of Random Matrices. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9022.","short":"G. Cipolloni, Fluctuations in the Spectrum of Random Matrices, Institute of Science and Technology Austria, 2021.","chicago":"Cipolloni, Giorgio. “Fluctuations in the Spectrum of Random Matrices.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9022."},"page":"380","date_published":"2021-01-25T00:00:00Z"},{"day":"14","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-09-14T00:00:00Z","citation":{"ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","apa":"Hensel, S. (2021). Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10007","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:10.15479/at:ista:10007","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10007.","mla":"Hensel, Sebastian. Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10007.","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021."},"page":"300","abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_size":15022154,"content_type":"application/x-zip-compressed","creator":"shensel","file_name":"thesis_final_Hensel.zip","access_level":"closed","date_updated":"2021-09-15T14:37:30Z","date_created":"2021-09-13T11:03:24Z","checksum":"c8475faaf0b680b4971f638f1db16347","relation":"source_file","file_id":"10008"},{"creator":"shensel","content_type":"application/pdf","file_size":6583638,"file_name":"thesis_final_Hensel.pdf","access_level":"open_access","date_updated":"2021-09-14T09:52:47Z","date_created":"2021-09-13T14:18:56Z","checksum":"1a609937aa5275452822f45f2da17f07","file_id":"10014","relation":"main_file"}],"_id":"10007","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["515"],"title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:10007","degree_awarded":"PhD","supervisor":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"file_date_updated":"2021-09-15T14:37:30Z","ec_funded":1,"author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10012"},{"id":"10013","status":"public","relation":"part_of_dissertation"},{"id":"7489","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-09-13T11:12:34Z","date_updated":"2023-09-07T13:30:45Z","year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"publisher":"Institute of Science and Technology Austria"},{"has_accepted_license":"1","article_processing_charge":"No","day":"22","date_published":"2021-09-22T00:00:00Z","citation":{"short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","mla":"Portinale, Lorenzo. Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10030.","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10030.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:10.15479/at:ista:10030","apa":"Portinale, L. (2021). Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10030","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria."},"abstract":[{"text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"8cd60dcb8762e8f21867e21e8001e183","date_created":"2021-09-21T09:17:34Z","date_updated":"2022-03-10T12:14:42Z","relation":"source_file","file_id":"10032","content_type":"application/x-zip-compressed","file_size":3876668,"creator":"cchlebak","access_level":"closed","file_name":"tex_and_pictures.zip"},{"relation":"main_file","file_id":"10047","checksum":"9789e9d967c853c1503ec7f307170279","date_created":"2021-09-27T11:14:31Z","date_updated":"2021-09-27T11:14:31Z","access_level":"open_access","file_name":"thesis_portinale_Final (1).pdf","file_size":2532673,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","status":"public","ddc":["515"],"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","_id":"10030","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"09","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.15479/at:ista:10030","project":[{"call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2022-03-10T12:14:42Z","date_created":"2021-09-21T09:14:15Z","date_updated":"2023-09-07T13:31:06Z","related_material":{"record":[{"id":"10022","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9792"},{"relation":"part_of_dissertation","status":"public","id":"7573"}]},"author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publication_status":"published","year":"2021","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245."},{"ddc":["539"],"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9920","oa_version":"Published Version","file":[{"checksum":"3cd1986efde5121d7581f6fcf9090da8","date_created":"2021-08-16T09:33:21Z","date_updated":"2021-09-06T08:39:47Z","file_id":"9924","relation":"source_file","creator":"mperuzzo","content_type":"application/x-zip-compressed","file_size":151387283,"access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip"},{"file_id":"9939","relation":"main_file","checksum":"50928c621cdf0775d7a5906b9dc8602c","date_created":"2021-08-18T14:20:06Z","date_updated":"2021-09-06T08:39:47Z","access_level":"open_access","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","creator":"mperuzzo","content_type":"application/pdf","file_size":17596344},{"file_id":"9940","relation":"other","checksum":"37f486aa1b622fe44af00d627ec13f6c","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:09Z","access_level":"closed","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","description":"Extra copy of the thesis as PDF/A-2b","creator":"mperuzzo","content_type":"application/pdf","file_size":17592425}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented."}],"page":"149","citation":{"chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920.","mla":"Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920"},"date_published":"2021-08-19T00:00:00Z","keyword":["quantum computing","superinductor","quantum metrology"],"day":"19","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"year":"2021","date_created":"2021-08-16T09:44:09Z","date_updated":"2023-09-07T13:31:22Z","author":[{"last_name":"Peruzzo","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"}],"related_material":{"record":[{"id":"9928","status":"public","relation":"part_of_dissertation"},{"id":"8755","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-09-06T08:39:47Z","oa":1,"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9920","month":"08","publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]}},{"title":"Underspecification in deep learning","ddc":["000"],"status":"public","_id":"9418","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"bphuong","file_size":2673905,"content_type":"application/pdf","file_name":"mph-thesis-v519-pdfimages.pdf","access_level":"open_access","date_created":"2021-05-24T11:22:29Z","date_updated":"2021-05-24T11:22:29Z","success":1,"checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_id":"9419","relation":"main_file"},{"access_level":"closed","file_name":"thesis.zip","creator":"bphuong","content_type":"application/zip","file_size":92995100,"file_id":"9420","relation":"source_file","checksum":"f5699e876bc770a9b0df8345a77720a2","date_updated":"2021-05-24T11:56:02Z","date_created":"2021-05-24T11:56:02Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"page":"125","citation":{"short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria."},"date_published":"2021-05-30T00:00:00Z","day":"30","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","year":"2021","date_created":"2021-05-24T13:06:23Z","date_updated":"2023-09-08T11:11:12Z","author":[{"first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"deleted","id":"7435"},{"relation":"part_of_dissertation","status":"public","id":"7481"},{"status":"public","relation":"part_of_dissertation","id":"9416"},{"id":"7479","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-05-24T11:56:02Z","oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9418","month":"05","publication_identifier":{"issn":["2663-337X"]}},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.","lang":"eng"}],"title":"Improved verification techniques for concurrent systems","ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10199","file":[{"checksum":"4f412a1ee60952221b499a4b1268df35","date_updated":"2021-11-08T14:12:22Z","date_created":"2021-11-08T14:12:22Z","file_id":"10225","relation":"main_file","creator":"vtoman","file_size":2915234,"content_type":"application/pdf","access_level":"open_access","file_name":"toman_th_final.pdf"},{"file_size":8616056,"content_type":"application/zip","creator":"vtoman","file_name":"toman_thesis.zip","access_level":"closed","date_updated":"2021-11-09T09:00:50Z","date_created":"2021-11-08T14:12:46Z","checksum":"9584943f99127be2dd2963f6784c37d4","relation":"source_file","file_id":"10226"}],"oa_version":"Published Version","keyword":["concurrency","verification","model checking"],"has_accepted_license":"1","article_processing_charge":"No","day":"31","page":"166","citation":{"chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10199.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","mla":"Toman, Viktor. Improved Verification Techniques for Concurrent Systems. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10199.","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021.","apa":"Toman, V. (2021). Improved verification techniques for concurrent systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10199","ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:10.15479/at:ista:10199"},"date_published":"2021-10-31T00:00:00Z","ec_funded":1,"file_date_updated":"2021-11-09T09:00:50Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","year":"2021","date_created":"2021-10-29T20:09:01Z","date_updated":"2023-09-19T09:59:54Z","related_material":{"record":[{"id":"10190","relation":"part_of_dissertation","status":"public"},{"id":"10191","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9987"},{"status":"public","relation":"part_of_dissertation","id":"141"}]},"author":[{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor"}],"publication_identifier":{"issn":["2663-337X"]},"month":"10","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"doi":"10.15479/at:ista:10199"},{"date_published":"2021-09-23T00:00:00Z","page":"276","citation":{"short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","apa":"Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035","ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria."},"has_accepted_license":"1","article_processing_charge":"No","day":"23","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":2104726,"content_type":"application/pdf","file_name":"thesis_pdfa.pdf","access_level":"open_access","date_updated":"2021-10-04T12:22:33Z","date_created":"2021-10-04T12:22:33Z","success":1,"checksum":"73a44345c683e81f3e765efbf86fdcc5","file_id":"10082","relation":"main_file"},{"checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","date_updated":"2022-03-10T12:15:18Z","date_created":"2021-10-05T07:04:37Z","relation":"source_file","file_id":"10085","file_size":9538359,"content_type":"application/x-zip-compressed","creator":"cchlebak","access_level":"closed","file_name":"thesis_final (1).zip"}],"status":"public","title":"On the adaptive security of graph-based games","ddc":["519"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10035","abstract":[{"lang":"eng","text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c])."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"doi":"10.15479/at:ista:10035","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09","date_updated":"2023-10-17T09:24:07Z","date_created":"2021-09-23T07:31:44Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10044"},{"id":"10049","relation":"part_of_dissertation","status":"public"},{"id":"637","status":"public","relation":"part_of_dissertation"},{"id":"10041","status":"public","relation":"part_of_dissertation"},{"id":"6430","relation":"part_of_dissertation","status":"public"},{"id":"10048","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published","acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","year":"2021","ec_funded":1,"file_date_updated":"2022-03-10T12:15:18Z"},{"day":"09","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-12-09T00:00:00Z","page":"132","citation":{"ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429."},"abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_Final_09_12_2021.pdf","creator":"gnadirad","content_type":"application/pdf","file_size":2370859,"file_id":"10436","relation":"main_file","success":1,"checksum":"6bf14e9a523387328f016c0689f5e10e","date_created":"2021-12-09T17:47:49Z","date_updated":"2021-12-09T17:47:49Z"},{"file_size":2596924,"content_type":"application/zip","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.zip","access_level":"closed","date_created":"2021-12-09T17:47:49Z","date_updated":"2022-03-28T12:55:12Z","checksum":"914d6c5ca86bd0add471971a8f4c4341","relation":"source_file","file_id":"10437"}],"ddc":["000"],"status":"public","title":"On achieving scalability through relaxation","_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"12","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10429","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"oa":1,"file_date_updated":"2022-03-28T12:55:12Z","ec_funded":1,"date_created":"2021-12-08T21:52:28Z","date_updated":"2023-10-17T11:48:55Z","author":[{"last_name":"Nadiradze","first_name":"Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi"}],"related_material":{"record":[{"id":"10432","status":"public","relation":"part_of_dissertation"},{"id":"6673","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5965"},{"id":"10435","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"year":"2021"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9733","status":"public","title":"The polaron at strong coupling","ddc":["515","519","539"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9944","date_updated":"2021-09-06T09:28:56Z","date_created":"2021-08-19T14:03:48Z","checksum":"e88bb8ca43948abe060eb2d2fa719881","file_name":"Thesis_FeliciangeliA.pdf","access_level":"open_access","file_size":1958710,"content_type":"application/pdf","creator":"dfelicia"},{"file_id":"9945","relation":"source_file","date_created":"2021-08-19T14:06:35Z","date_updated":"2022-03-10T12:13:57Z","checksum":"72810843abee83705853505b3f8348aa","file_name":"thesis.7z","access_level":"closed","creator":"dfelicia","content_type":"application/octet-stream","file_size":3771669}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.","lang":"eng"}],"citation":{"ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021."},"page":"180","date_published":"2021-08-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","year":"2021","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"id":"9792","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9225"},{"relation":"part_of_dissertation","status":"public","id":"9781"},{"id":"9791","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"}],"date_updated":"2024-03-06T12:30:44Z","date_created":"2021-07-27T15:48:30Z","ec_funded":1,"file_date_updated":"2022-03-10T12:13:57Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"doi":"10.15479/at:ista:9733","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"},{"first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"08"},{"ec_funded":1,"file_date_updated":"2021-09-15T22:30:26Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2021","date_created":"2021-09-09T07:37:20Z","date_updated":"2023-09-07T13:38:33Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6351"},{"id":"6943","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8002"}]},"author":[{"first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15479/at:ista:9992","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"status":"public","ddc":["575"],"title":"Wound healing in the Arabidopsis root meristem","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9992","oa_version":"Published Version","file":[{"creator":"lhoermaye","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25179004,"access_level":"closed","file_name":"Thesis_vupload.docx","embargo_to":"open_access","checksum":"c763064adaa720e16066c1a4f9682bbb","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T07:29:48Z","file_id":"9993","relation":"source_file"},{"date_created":"2021-09-09T14:25:08Z","date_updated":"2021-09-15T22:30:26Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","relation":"main_file","embargo":"2021-09-09","file_id":"9996","file_size":6246900,"content_type":"application/pdf","creator":"lhoermaye","file_name":"Thesis_vfinal_pdfa.pdf","access_level":"open_access"}],"has_accepted_license":"1","article_processing_charge":"No","day":"13","page":"168","citation":{"ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"date_published":"2021-09-13T00:00:00Z"},{"page":"111","citation":{"ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623."},"date_published":"2021-07-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","status":"public","ddc":["570"],"_id":"9623","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":131946790,"creator":"scaballe","access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_SCM.docx","checksum":"e039225a47ef32666d59bf35ddd30ecf","date_created":"2021-07-01T14:48:54Z","date_updated":"2022-07-02T22:30:06Z","relation":"source_file","file_id":"9624"},{"date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:46:25Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","embargo":"2022-07-01","relation":"main_file","creator":"scaballe","content_type":"application/pdf","file_size":17094958,"file_name":"PhDThesis_SCM.pdf","access_level":"open_access"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9623","month":"07","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","year":"2021","date_created":"2021-07-01T14:50:17Z","date_updated":"2023-09-07T13:33:27Z","author":[{"last_name":"Caballero Mancebo","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9750"},{"status":"public","relation":"part_of_dissertation","id":"9006"}]},"file_date_updated":"2022-07-02T22:30:06Z"},{"publication_identifier":{"issn":["2663-337X"]},"month":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"}],"doi":"10.15479/at:ista:10058","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"file_date_updated":"2022-12-20T23:30:07Z","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","year":"2021","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"8831","relation":"part_of_dissertation","status":"public"},{"id":"10065","status":"public","relation":"part_of_dissertation"},{"id":"10066","relation":"part_of_dissertation","status":"public"},{"id":"8909","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5816"}]},"author":[{"full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"}],"date_created":"2021-09-30T07:53:49Z","date_updated":"2023-09-08T11:41:08Z","keyword":["qubits","quantum computing","holes"],"article_processing_charge":"No","has_accepted_license":"1","day":"05","citation":{"ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058."},"page":"151","date_published":"2021-10-05T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10058","title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","status":"public","ddc":["621","539"],"file":[{"access_level":"closed","file_name":"PHD_Thesis_Jirovec_Source.zip","embargo_to":"open_access","creator":"djirovec","content_type":"application/x-zip-compressed","file_size":32397600,"file_id":"10061","relation":"source_file","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-09-30T14:29:14Z"},{"file_id":"10087","embargo":"2022-10-06","relation":"main_file","date_created":"2021-10-05T07:56:49Z","date_updated":"2022-12-20T23:30:07Z","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_name":"PHD_Thesis_pdfa2b_1.pdf","access_level":"open_access","creator":"djirovec","content_type":"application/pdf","file_size":26910829}],"oa_version":"Published Version"},{"day":"18","has_accepted_license":"1","article_processing_charge":"No","page":"101","citation":{"short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria."},"date_published":"2021-05-18T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"status":"public","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","ddc":["571"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9397","file":[{"file_name":"KHuljev_Thesis_corrections.docx","embargo_to":"open_access","access_level":"closed","creator":"khuljev","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47799741,"file_id":"9398","relation":"source_file","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","checksum":"7f98532f5324a0b2f3fa8de2967baa19"},{"creator":"khuljev","content_type":"application/pdf","file_size":16542131,"access_level":"open_access","file_name":"new_KHuljev_Thesis_corrections.pdf","checksum":"bf512f8a1e572a543778fc4b227c01ba","date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-18T14:50:28Z","file_id":"9401","embargo":"2022-05-20","relation":"main_file"}],"oa_version":"Published Version","month":"05","publication_identifier":{"issn":["2663-337X"]},"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9397","file_date_updated":"2022-05-21T22:30:04Z","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","year":"2021","date_created":"2021-05-17T12:31:30Z","date_updated":"2023-09-07T13:32:32Z","author":[{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla"}]},{"oa_version":"Published Version","file":[{"embargo":"2022-07-01","file_id":"9563","relation":"main_file","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z","checksum":"659df5518db495f679cb1df9e9bd1d94","file_name":"Thesis.pdf","access_level":"open_access","creator":"dkleindienst","content_type":"application/pdf","file_size":77299142},{"file_id":"9564","relation":"source_file","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","checksum":"3bcf63a2b19e5b6663be051bea332748","file_name":"Thesis_source.zip","embargo_to":"open_access","access_level":"closed","creator":"dkleindienst","file_size":369804895,"content_type":"application/zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9562","ddc":["570"],"status":"public","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","abstract":[{"lang":"eng","text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-06-01T00:00:00Z","citation":{"short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria."},"page":"124","has_accepted_license":"1","article_processing_charge":"No","day":"01","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9756"},{"relation":"part_of_dissertation","status":"public","id":"9437"},{"id":"8532","relation":"part_of_dissertation","status":"public"},{"id":"612","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David"}],"date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","year":"2021","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publication_status":"published","file_date_updated":"2022-07-02T22:30:04Z","doi":"10.15479/at:ista:9562","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06"},{"oa_version":"Published Version","file":[{"file_name":"Thesis-pdfa.pdf","access_level":"open_access","file_size":5251507,"content_type":"application/pdf","creator":"akafshda","relation":"main_file","embargo":"2021-12-22","file_id":"8969","date_created":"2020-12-22T20:08:44Z","date_updated":"2021-12-23T23:30:04Z","checksum":"d1b9db3725aed34dadd81274aeb9426c"},{"relation":"source_file","file_id":"8970","checksum":"1661df7b393e6866d2460eba3c905130","date_created":"2020-12-22T20:08:50Z","date_updated":"2021-03-04T23:30:04Z","access_level":"closed","embargo_to":"open_access","file_name":"source.zip","content_type":"application/zip","file_size":10636756,"creator":"akafshda"}],"ddc":["005"],"status":"public","title":"Parameterized and algebro-geometric advances in static program analysis","_id":"8934","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-01-01T00:00:00Z","page":"278","citation":{"short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"01","date_created":"2020-12-10T12:17:07Z","date_updated":"2023-09-22T10:03:21Z","related_material":{"record":[{"id":"1386","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"id":"311","status":"public","relation":"part_of_dissertation"},{"id":"6056","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6380"},{"relation":"part_of_dissertation","status":"public","id":"639"},{"relation":"part_of_dissertation","status":"public","id":"66"},{"id":"6780","status":"public","relation":"part_of_dissertation"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"id":"7810","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6175"},{"relation":"part_of_dissertation","status":"public","id":"6378"},{"relation":"part_of_dissertation","status":"public","id":"6490"},{"id":"7014","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8089"},{"id":"8728","relation":"part_of_dissertation","status":"public"},{"id":"7158","status":"public","relation":"part_of_dissertation"},{"id":"5977","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"relation":"part_of_dissertation","status":"public","id":"6340"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","year":"2021","license":"https://creativecommons.org/publicdomain/zero/1.0/","file_date_updated":"2021-12-23T23:30:04Z","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8934","project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"01"},{"day":"18","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307"},"page":"73","date_published":"2021-11-18T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"_id":"10307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Pathogenic Escherichia coli hijack the host immune response","status":"public","file":[{"date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:31Z","checksum":"b39c9e0ef18d0484d537a67551effd02","file_id":"10308","embargo":"2022-11-18","relation":"main_file","creator":"ktomasek","content_type":"application/pdf","file_size":13266088,"file_name":"ThesisTomasekKathrin.pdf","access_level":"open_access"},{"file_size":7539509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ktomasek","embargo_to":"open_access","file_name":"ThesisTomasekKathrin.docx","access_level":"closed","date_created":"2021-11-18T15:07:46Z","date_updated":"2022-12-20T23:30:05Z","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","relation":"source_file","file_id":"10309"}],"oa_version":"Published Version","month":"11","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/at:ista:10307","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"language":[{"iso":"eng"}],"file_date_updated":"2022-12-20T23:30:05Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"author":[{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek"}],"related_material":{"record":[{"id":"10316","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-11-18T15:05:06Z","date_updated":"2023-09-07T13:34:38Z"},{"day":"22","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-11-22T00:00:00Z","page":"139","citation":{"chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303"},"abstract":[{"text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_created":"2021-11-22T14:48:21Z","date_updated":"2022-12-20T23:30:06Z","checksum":"dea38b98aa4da1cea03dcd0f10862818","relation":"main_file","embargo":"2022-11-23","file_id":"10331","file_size":28005730,"content_type":"application/pdf","creator":"rabualia","file_name":"AbualiaPhDthesisfinalv3.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"10332","date_created":"2021-11-22T14:48:34Z","date_updated":"2022-12-20T23:30:06Z","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","embargo_to":"open_access","file_name":"AbualiaPhDthesisfinalv3.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":62841883,"creator":"rabualia"}],"ddc":["580","581"],"status":"public","title":"Role of hormones in nitrate regulated growth","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10303","month":"11","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10303","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2022-12-20T23:30:06Z","date_updated":"2023-09-19T14:42:45Z","date_created":"2021-11-18T11:20:59Z","author":[{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","first_name":"Rashed","last_name":"Abualia"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9010"},{"id":"9913","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"47"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"year":"2021"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"doi":"10.15479/at:ista:9962","supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8569"},{"id":"960","status":"public","relation":"part_of_dissertation"}]},"date_created":"2021-08-29T12:36:50Z","date_updated":"2023-09-22T09:58:30Z","file_date_updated":"2022-09-03T22:30:04Z","citation":{"ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021."},"page":"182","date_published":"2021-09-02T00:00:00Z","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"day":"02","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9962","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"9971","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-30T09:17:39Z","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","file_size":10629190,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ahansen"},{"relation":"main_file","embargo":"2022-09-02","file_id":"9972","date_created":"2021-08-30T09:29:44Z","date_updated":"2022-09-03T22:30:04Z","checksum":"204fa40321a1c6289b68c473634c4bf3","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","content_type":"application/pdf","file_size":13457469,"creator":"ahansen"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"06","date_published":"2021-10-06T00:00:00Z","citation":{"ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083."},"abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","creator":"cchlebak","file_size":8616142,"content_type":"application/pdf","embargo":"2022-10-14","file_id":"10138","relation":"main_file","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:07Z"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":15058499,"creator":"cchlebak","embargo_to":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","access_level":"closed","date_created":"2021-10-14T08:00:13Z","date_updated":"2022-12-20T23:30:03Z","checksum":"f23ed258ca894f6aabf58b0c128bf242","relation":"source_file","file_id":"10139"}],"_id":"10083","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Rapid cell growth regulation in Arabidopsis","ddc":["575"],"publication_identifier":{"issn":["2663-337X"]},"month":"10","doi":"10.15479/at:ista:10083","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"ec_funded":1,"file_date_updated":"2022-12-20T23:30:03Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"442"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"9287"},{"status":"public","relation":"part_of_dissertation","id":"8283"},{"relation":"part_of_dissertation","status":"public","id":"8986"},{"relation":"part_of_dissertation","status":"public","id":"6627"},{"id":"10095","relation":"part_of_dissertation","status":"public"},{"id":"10015","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"date_updated":"2023-10-31T19:30:02Z","date_created":"2021-10-04T13:33:10Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"year":"2021","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9997"},{"relation":"part_of_dissertation","status":"public","id":"2"},{"status":"public","relation":"part_of_dissertation","id":"9402"}]},"author":[{"first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"}],"date_updated":"2023-11-07T08:28:29Z","date_created":"2021-11-15T17:12:57Z","ec_funded":1,"file_date_updated":"2022-12-20T23:30:08Z","oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:10293","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"11","_id":"10293","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","status":"public","ddc":["519","576"],"oa_version":"Published Version","file":[{"checksum":"86a05b430756ca12ae8107b6e6f3c1e5","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-18T12:41:46Z","relation":"source_file","file_id":"10305","file_size":29703124,"content_type":"application/zip","creator":"lschmid","access_level":"closed","embargo_to":"open_access","file_name":"submission_new.zip"},{"checksum":"d940af042e94660c6b6a7b4f0b184d47","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-18T12:59:15Z","file_id":"10306","embargo":"2022-10-18","relation":"main_file","creator":"lschmid","content_type":"application/pdf","file_size":8320985,"access_level":"open_access","file_name":"thesis_new_upload.pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient."}],"citation":{"short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria."},"page":"171","date_published":"2021-11-17T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"17"},{"file":[{"access_level":"closed","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","embargo_to":"open_access","creator":"cziletti","file_size":28508629,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10186","relation":"source_file","checksum":"ce7108853e6cec6224f17cd6429b51fe","date_created":"2021-10-27T07:45:37Z","date_updated":"2022-12-20T23:30:05Z"},{"checksum":"0d7afb846e8e31ec794de47bf44e12ef","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-10-27T07:45:57Z","relation":"main_file","file_id":"10187","embargo":"2022-10-28","content_type":"application/pdf","file_size":10623525,"creator":"cziletti","access_level":"open_access","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10135","title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","status":"public","ddc":["570"],"abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-10-13T00:00:00Z","citation":{"mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135"},"day":"13","has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Semerádová","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semerádová, Hana"}],"related_material":{"record":[{"id":"9160","relation":"part_of_dissertation","status":"public"}]},"date_created":"2021-10-13T13:42:48Z","date_updated":"2024-01-25T10:53:29Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:05Z","doi":"10.15479/at:ista:10135","degree_awarded":"PhD","supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746"}],"month":"10","publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]}},{"month":"07","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9728","acknowledged_ssus":[{"_id":"M-Shop"}],"supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2022-07-29T22:30:05Z","author":[{"last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal"}],"related_material":{"record":[{"id":"6189","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2024-02-28T13:14:39Z","date_created":"2021-07-27T13:40:30Z","year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"day":"29","has_accepted_license":"1","article_processing_charge":"No","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"date_published":"2021-07-29T00:00:00Z","citation":{"chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728.","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728"},"page":"118","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"creator":"nagrawal","file_size":22859658,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","embargo_to":"open_access","checksum":"77436be3563a90435024307b1b5ee7e8","date_created":"2021-07-28T13:32:02Z","date_updated":"2022-07-29T22:30:05Z","file_id":"9744","relation":"source_file"},{"date_updated":"2022-07-29T22:30:05Z","date_created":"2021-07-28T13:32:05Z","checksum":"72a891d7daba85445c29b868c22575ed","relation":"main_file","file_id":"9745","embargo":"2022-07-28","file_size":18658048,"content_type":"application/pdf","creator":"nagrawal","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"9728","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","status":"public","ddc":["532"]},{"month":"03","publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"oa":1,"supervisor":[{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7629","file_date_updated":"2020-07-14T12:48:01Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JaMa"}],"year":"2020","date_created":"2020-04-02T06:40:23Z","date_updated":"2023-09-07T13:03:12Z","author":[{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","last_name":"Forkert"}],"day":"31","has_accepted_license":"1","article_processing_charge":"No","page":"154","citation":{"ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629."},"date_published":"2020-03-31T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","status":"public","ddc":["510"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7629","file":[{"relation":"main_file","file_id":"7657","date_created":"2020-04-14T10:47:59Z","date_updated":"2020-07-14T12:48:01Z","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_name":"Thesis_Forkert_PDFA.pdf","access_level":"open_access","file_size":3297129,"content_type":"application/pdf","creator":"dernst"},{"file_id":"7658","relation":"source_file","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","date_created":"2020-04-14T10:47:59Z","date_updated":"2020-07-14T12:48:01Z","access_level":"closed","file_name":"Thesis_Forkert_source.zip","creator":"dernst","file_size":1063908,"content_type":"application/x-zip-compressed"}],"oa_version":"Published Version"},{"publication_identifier":{"issn":["2663-337X"]},"month":"02","doi":"10.15479/AT:ISTA:7514","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7524"}]},"author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon"}],"date_updated":"2023-09-07T13:12:42Z","date_created":"2020-02-24T09:17:27Z","year":"2020","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"24","date_published":"2020-02-24T00:00:00Z","citation":{"ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020."},"page":"148","abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"creator":"dernst","file_size":1563429,"content_type":"application/pdf","access_level":"open_access","file_name":"thesis.pdf","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","date_created":"2020-02-24T09:15:06Z","date_updated":"2020-07-14T12:47:59Z","file_id":"7515","relation":"main_file"},{"relation":"source_file","file_id":"7516","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-24T09:15:16Z","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_name":"thesis_source.zip","access_level":"closed","file_size":2028038,"content_type":"application/x-zip-compressed","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7514","title":"The free energy of a dilute two-dimensional Bose gas","status":"public","ddc":["510"]},{"date_published":"2020-09-09T00:00:00Z","page":"191","citation":{"short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria."},"day":"09","article_processing_charge":"No","has_accepted_license":"1","file":[{"access_level":"open_access","file_name":"Thesis_Julia_Steiner_pdfA.pdf","creator":"jsteiner","file_size":117547589,"content_type":"application/pdf","file_id":"8354","relation":"main_file","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","date_created":"2020-09-09T14:22:35Z"},{"checksum":"ba112f957b7145462d0ab79044873ee9","date_created":"2020-09-09T14:23:25Z","date_updated":"2020-09-15T08:48:37Z","relation":"source_file","file_id":"8355","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":223328668,"creator":"jsteiner","access_level":"closed","file_name":"Thesis_Julia_Steiner.docx"}],"oa_version":"None","ddc":["572"],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","status":"public","_id":"8353","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"supervisor":[{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8353","project":[{"name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741","_id":"26169496-B435-11E9-9278-68D0E5697425"}],"oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]},"date_created":"2020-09-09T14:27:01Z","date_updated":"2023-09-07T13:14:09Z","author":[{"last_name":"Steiner","first_name":"Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","full_name":"Steiner, Julia"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8284"}]},"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","year":"2020","file_date_updated":"2021-09-16T12:40:56Z"},{"acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7643"}]},"author":[{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-09-30T14:50:51Z","date_updated":"2023-09-07T13:13:05Z","file_date_updated":"2021-10-01T13:33:02Z","oa":1,"doi":"10.15479/AT:ISTA:8589","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"09","_id":"8589","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Novel insights into PIN polarity regulation during Arabidopsis development","status":"public","ddc":["580"],"oa_version":"Published Version","file":[{"creator":"dernst","file_size":49198118,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2020_Han_Thesis.docx","checksum":"c4bda1947d4c09c428ac9ce667b02327","date_created":"2020-09-30T14:50:20Z","date_updated":"2020-09-30T14:50:20Z","file_id":"8590","relation":"source_file"},{"creator":"dernst","file_size":15513963,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Han_Thesis.pdf","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","date_created":"2020-09-30T14:49:59Z","date_updated":"2021-10-01T13:33:02Z","file_id":"8591","relation":"main_file"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development."}],"citation":{"chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589"},"page":"164","date_published":"2020-09-30T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"30"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8155","title":"Gene regulation across scales – how biophysical constraints shape evolution","ddc":["530","570"],"status":"public","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","content_type":"application/pdf","file_size":16638998,"creator":"rgrah","relation":"main_file","file_id":"8176","success":1,"date_created":"2020-07-27T12:00:07Z","date_updated":"2020-07-27T12:00:07Z"},{"relation":"main_file","file_id":"8177","date_updated":"2020-07-30T13:04:55Z","date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip","access_level":"closed","file_size":347459978,"content_type":"application/zip","creator":"rgrah"}],"article_processing_charge":"No","has_accepted_license":"1","day":"24","citation":{"ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155."},"page":"310","date_published":"2020-07-24T00:00:00Z","file_date_updated":"2020-07-30T13:04:55Z","year":"2020","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"7675","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7569"},{"id":"7652","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah"}],"date_created":"2020-07-23T09:51:28Z","date_updated":"2023-09-07T13:13:27Z","publication_identifier":{"issn":["2663-337X"]},"month":"07","oa":1,"project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:8155","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD"},{"day":"10","has_accepted_license":"1","article_processing_charge":"No","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"date_published":"2020-02-10T00:00:00Z","page":"155","citation":{"ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460."},"abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"thesis_ist-final_noack.pdf","creator":"koelsboe","file_size":76195184,"content_type":"application/pdf","file_id":"7461","relation":"main_file","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:43:54Z"},{"relation":"source_file","file_id":"7462","date_created":"2020-02-06T14:52:45Z","date_updated":"2020-07-14T12:47:58Z","checksum":"7a52383c812b0be64d3826546509e5a4","file_name":"latex-files.zip","description":"latex source files, figures","access_level":"closed","content_type":"application/x-zip-compressed","file_size":122103715,"creator":"koelsboe"}],"status":"public","ddc":["514"],"title":"The hole system of triangulated shapes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7460","month":"02","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7460","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"file_date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:56:53Z","date_updated":"2023-09-07T13:15:30Z","author":[{"full_name":"Ölsböck, Katharina","last_name":"Ölsböck","first_name":"Katharina","orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6608","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"year":"2020"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7896","status":"public","ddc":["000"],"title":"On the average-case hardness of total search problems","oa_version":"Published Version","file":[{"file_name":"2020_Thesis_Kamath.pdf","access_level":"open_access","file_size":1622742,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7897","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:13Z","checksum":"b39e2e1c376f5819b823fb7077491c64"},{"checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:23Z","relation":"source_file","file_id":"7898","file_size":15301529,"content_type":"application/x-zip-compressed","creator":"dernst","access_level":"closed","file_name":"Thesis_Kamath.zip"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"citation":{"short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria."},"page":"126","date_published":"2020-05-25T00:00:00Z","day":"25","has_accepted_license":"1","article_processing_charge":"No","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"}],"related_material":{"record":[{"id":"6677","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T13:15:55Z","date_created":"2020-05-26T14:08:55Z","file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"doi":"10.15479/AT:ISTA:7896","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["2663-337X"]}},{"language":[{"iso":"eng"}],"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7944","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"month":"06","date_updated":"2023-09-07T13:17:37Z","date_created":"2020-06-08T00:49:46Z","related_material":{"record":[{"id":"7950","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"5986"}]},"author":[{"orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana","full_name":"Masárová, Zuzana"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"publication_status":"published","year":"2020","license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2020-07-14T12:48:05Z","date_published":"2020-06-09T00:00:00Z","page":"160","citation":{"ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020."},"article_processing_charge":"No","has_accepted_license":"1","day":"09","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"file":[{"file_name":"THESIS_Zuzka_Masarova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":13661779,"creator":"zmasarov","relation":"main_file","file_id":"7945","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T00:34:00Z","checksum":"df688bc5a82b50baee0b99d25fc7b7f0"},{"date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T00:35:30Z","checksum":"45341a35b8f5529c74010b7af43ac188","relation":"source_file","file_id":"7946","file_size":32184006,"content_type":"application/zip","creator":"zmasarov","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","access_level":"closed"}],"oa_version":"Published Version","title":"Reconfiguration problems","ddc":["516","514"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7944","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"file_date_updated":"2021-09-16T12:49:12Z","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","year":"2020","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7580"}]},"author":[{"orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","last_name":"Bezeljak","first_name":"Urban","full_name":"Bezeljak, Urban"}],"date_created":"2020-09-08T08:53:53Z","date_updated":"2023-09-07T13:17:06Z","publication_identifier":{"issn":["2663-337X"]},"month":"09","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:8341","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"supervisor":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"_id":"8341","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"In vitro reconstitution of a Rab activation switch","status":"public","ddc":["570"],"file":[{"creator":"dernst","content_type":"application/x-zip-compressed","file_size":65246782,"access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","date_created":"2020-09-08T09:00:29Z","file_id":"8342","relation":"source_file"},{"date_created":"2020-09-08T09:00:27Z","date_updated":"2021-09-16T12:49:12Z","checksum":"59a62275088b00b7241e6ff4136434c7","file_id":"8343","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":31259058,"file_name":"2020_Urban_Bezeljak_Thesis.pdf","access_level":"open_access"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"08","citation":{"ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341."},"page":"215","date_published":"2020-09-08T00:00:00Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:8032","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"month":"06","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"id":"6556","status":"public","relation":"dissertation_contains"},{"id":"7093","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Kristóf","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf"}],"date_updated":"2023-09-07T13:18:27Z","date_created":"2020-06-26T10:00:36Z","file_date_updated":"2020-07-14T12:48:08Z","citation":{"ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020."},"page":"xviii+120","date_published":"2020-06-26T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8032","title":"Combinatorial width parameters for 3-dimensional manifolds","status":"public","ddc":["514"],"oa_version":"Published Version","file":[{"file_name":"Kristof_Huszar-Thesis.pdf","access_level":"open_access","file_size":2637562,"content_type":"application/pdf","creator":"khuszar","relation":"main_file","file_id":"8034","date_created":"2020-06-26T10:03:58Z","date_updated":"2020-07-14T12:48:08Z","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3"},{"file_id":"8035","relation":"source_file","checksum":"d5f8456202b32f4a77552ef47a2837d1","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-26T10:10:06Z","access_level":"closed","file_name":"Kristof_Huszar-Thesis-source.zip","creator":"khuszar","content_type":"application/x-zip-compressed","file_size":7163491}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}]},{"author":[{"orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R"}],"related_material":{"record":[{"id":"7572","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7197"}]},"date_updated":"2023-09-07T13:18:51Z","date_created":"2020-09-10T09:26:49Z","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","year":"2020","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-09-11T07:48:10Z","doi":"10.15479/AT:ISTA:8358","supervisor":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"}],"acknowledged_ssus":[{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"09","publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"oa_version":"Published Version","file":[{"file_id":"8364","relation":"main_file","date_created":"2020-09-10T12:11:29Z","date_updated":"2020-09-10T12:11:29Z","success":1,"checksum":"882f93fe9c351962120e2669b84bf088","file_name":"phd_thesis_pcaldas.pdf","access_level":"open_access","creator":"pcaldas","content_type":"application/pdf","file_size":141602462},{"file_name":"phd_thesis_latex_pcaldas.zip","access_level":"closed","creator":"pcaldas","file_size":450437458,"content_type":"application/x-zip-compressed","file_id":"8365","relation":"source_file","date_updated":"2020-09-11T07:48:10Z","date_created":"2020-09-10T12:18:17Z","checksum":"70cc9e399c4e41e6e6ac445ae55e8558"}],"_id":"8358","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","ddc":["572"],"status":"public","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-10T00:00:00Z","citation":{"ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358."},"page":"135","day":"10","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Published Version","file":[{"checksum":"26fe261550f691280bda4c454bf015c7","date_updated":"2020-09-04T12:17:47Z","date_created":"2020-09-04T12:17:47Z","file_id":"8333","relation":"main_file","creator":"bkragl","content_type":"application/pdf","file_size":1348815,"access_level":"open_access","file_name":"kragl-thesis.pdf"},{"file_size":372312,"content_type":"application/zip","creator":"bkragl","access_level":"closed","file_name":"kragl-thesis.zip","checksum":"b9694ce092b7c55557122adba8337ebc","date_created":"2020-09-04T13:00:17Z","date_updated":"2020-09-04T13:00:17Z","relation":"source_file","file_id":"8335"}],"_id":"8332","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["000"],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-03T00:00:00Z","citation":{"ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332."},"page":"120","day":"03","has_accepted_license":"1","article_processing_charge":"No","author":[{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"}],"related_material":{"record":[{"id":"133","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8012"},{"relation":"part_of_dissertation","status":"public","id":"8195"},{"id":"160","status":"public","relation":"part_of_dissertation"}]},"date_created":"2020-09-04T12:24:12Z","date_updated":"2023-09-13T08:45:08Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","doi":"10.15479/AT:ISTA:8332","degree_awarded":"PhD","supervisor":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"}],"language":[{"iso":"eng"}],"oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]}},{"citation":{"chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958"},"page":"125","date_published":"2020-12-21T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8958","ddc":["539"],"status":"public","title":"Rotation of coupled cold molecules in the presence of a many-body environment","oa_version":"Published Version","file":[{"file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","creator":"xli","content_type":"application/pdf","file_size":3622305,"file_id":"8967","relation":"main_file","date_updated":"2020-12-22T10:55:56Z","date_created":"2020-12-22T10:55:56Z","success":1,"checksum":"3994c54a1241451d561db1d4f43bad30"},{"file_name":"THESIS_Xiang_Li.zip","access_level":"closed","file_size":4018859,"content_type":"application/x-zip-compressed","creator":"xli","relation":"source_file","file_id":"8968","date_created":"2020-12-22T10:56:03Z","date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"oa":1,"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:8958","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"12","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiLe"}],"publication_status":"published","related_material":{"record":[{"id":"5886","relation":"part_of_dissertation","status":"public"},{"id":"8587","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1120"}]},"author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Xiang","full_name":"Li, Xiang"}],"date_created":"2020-12-21T09:44:30Z","date_updated":"2023-09-20T11:30:58Z","ec_funded":1,"file_date_updated":"2020-12-30T07:18:03Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"14","page":"148","citation":{"chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386"},"date_published":"2020-09-14T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}],"ddc":["003"],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8386","oa_version":"Published Version","file":[{"file_id":"8388","relation":"source_file","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","date_updated":"2020-09-14T12:18:43Z","date_created":"2020-09-14T01:02:59Z","access_level":"closed","file_name":"Thesis_Ran.zip","creator":"rzhang","content_type":"application/x-zip-compressed","file_size":1245800191},{"file_size":161385316,"content_type":"application/pdf","creator":"rzhang","access_level":"open_access","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","checksum":"817e20c33be9247f906925517c56a40d","success":1,"date_created":"2020-09-15T12:51:53Z","date_updated":"2020-09-15T12:51:53Z","relation":"main_file","file_id":"8396"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","project":[{"name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8386","ec_funded":1,"file_date_updated":"2020-09-15T12:51:53Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"publication_status":"published","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","year":"2020","date_created":"2020-09-14T01:04:53Z","date_updated":"2023-09-22T09:49:31Z","related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"id":"1002","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Zhang, Ran","last_name":"Zhang","first_name":"Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87"}]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity."}],"status":"public","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","ddc":["530"],"_id":"7996","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7997","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","date_created":"2020-06-22T09:22:04Z","date_updated":"2020-07-14T12:48:07Z","access_level":"closed","file_name":"JK_thesis_latex_source_files.zip","file_size":392794743,"content_type":"application/x-zip-compressed","creator":"dernst"},{"access_level":"open_access","file_name":"PhD_thesis_JK_pdfa.pdf","creator":"dernst","content_type":"application/pdf","file_size":28453247,"file_id":"7998","relation":"main_file","checksum":"1de716bf110dbd77d383e479232bf496","date_updated":"2020-07-14T12:48:07Z","date_created":"2020-06-22T09:21:29Z"}],"day":"22","has_accepted_license":"1","article_processing_charge":"No","page":"178","citation":{"short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria."},"date_published":"2020-06-22T00:00:00Z","file_date_updated":"2020-07-14T12:48:07Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"year":"2020","date_created":"2020-06-22T09:22:23Z","date_updated":"2023-09-26T15:50:22Z","author":[{"first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"}],"related_material":{"record":[{"id":"1328","relation":"part_of_dissertation","status":"public"},{"id":"7541","status":"public","relation":"part_of_dissertation"},{"id":"77","relation":"part_of_dissertation","status":"public"},{"id":"23","relation":"part_of_dissertation","status":"public"},{"id":"840","relation":"part_of_dissertation","status":"public"}]},"month":"06","publication_identifier":{"issn":["2663-337X"]},"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7996"},{"file_date_updated":"2020-09-14T13:39:17Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"publication_status":"published","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","year":"2020","date_created":"2020-09-14T13:42:09Z","date_updated":"2023-10-16T10:04:02Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7936"},{"relation":"part_of_dissertation","status":"public","id":"7937"},{"id":"8193","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"relation":"part_of_dissertation","status":"public","id":"911"}]},"author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705","first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie"}],"publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"month":"09","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8390","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. ","lang":"eng"}],"ddc":["000"],"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8390","file":[{"relation":"main_file","file_id":"8391","date_updated":"2020-09-14T13:39:14Z","date_created":"2020-09-14T13:39:14Z","checksum":"c914d2f88846032f3d8507734861b6ee","success":1,"file_name":"2020_Thesis_Royer.pdf","access_level":"open_access","file_size":30224591,"content_type":"application/pdf","creator":"dernst"},{"file_id":"8392","relation":"main_file","checksum":"ae98fb35d912cff84a89035ae5794d3c","date_updated":"2020-09-14T13:39:17Z","date_created":"2020-09-14T13:39:17Z","access_level":"closed","file_name":"thesis_sources.zip","creator":"dernst","file_size":74227627,"content_type":"application/x-zip-compressed"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"14","page":"197","citation":{"chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390"},"date_published":"2020-09-14T00:00:00Z"},{"file_date_updated":"2020-07-27T12:46:53Z","date_updated":"2023-12-18T10:51:01Z","date_created":"2020-07-23T09:51:29Z","author":[{"first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey"}],"related_material":{"record":[{"id":"8182","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8183"},{"status":"public","relation":"part_of_dissertation","id":"8185"},{"id":"8184","relation":"part_of_dissertation","status":"public"},{"id":"6355","status":"public","relation":"part_of_dissertation"},{"id":"75","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"year":"2020","month":"07","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8156","oa":1,"abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"8178","date_updated":"2020-07-27T12:44:51Z","date_created":"2020-07-27T12:44:51Z","access_level":"closed","file_name":"source.zip","file_size":1061740,"content_type":"application/zip","creator":"savvakum"},{"creator":"savvakum","file_size":1336501,"content_type":"application/pdf","access_level":"open_access","file_name":"thesis_pdfa.pdf","success":1,"date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-27T12:46:53Z","file_id":"8179","relation":"main_file"}],"oa_version":"Published Version","title":"Topological methods in geometry and discrete mathematics","ddc":["514"],"status":"public","_id":"8156","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"24","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-07-24T00:00:00Z","page":"119","citation":{"ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156."}},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop.","lang":"eng"}],"_id":"8366","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Computational design of curved thin shells: From glass façades to programmable matter","ddc":["000"],"file":[{"relation":"main_file","file_id":"8367","date_created":"2020-09-10T16:11:49Z","date_updated":"2020-09-10T16:11:49Z","checksum":"f8da89553da36037296b0a80f14ebf50","success":1,"file_name":"thesis_rguseinov.pdf","access_level":"open_access","content_type":"application/pdf","file_size":70950442,"creator":"rguseino"},{"creator":"rguseino","file_size":76207597,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"thesis_source.zip","checksum":"e8fd944c960c20e0e27e6548af69121d","date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-11T09:39:48Z","file_id":"8374","relation":"source_file"}],"oa_version":"Published Version","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"has_accepted_license":"1","article_processing_charge":"No","day":"21","citation":{"chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366"},"page":"118","date_published":"2020-09-21T00:00:00Z","ec_funded":1,"file_date_updated":"2020-09-16T15:11:01Z","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"deleted","id":"7151"},{"status":"public","relation":"part_of_dissertation","id":"7262"},{"id":"8562","relation":"part_of_dissertation","status":"public"},{"id":"1001","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"research_data","id":"8375"}]},"author":[{"full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","first_name":"Ruslan"}],"date_updated":"2024-02-21T12:44:29Z","date_created":"2020-09-10T16:19:55Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"month":"09","oa":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:8366","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}]},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/AT:ISTA:7525","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"02","date_updated":"2023-09-07T13:20:03Z","date_created":"2020-02-26T10:56:37Z","author":[{"last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"RySh"}],"publication_status":"published","year":"2020","file_date_updated":"2021-03-01T23:30:04Z","date_published":"2020-02-28T00:00:00Z","page":"79","citation":{"ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525.","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525."},"article_processing_charge":"No","has_accepted_license":"1","day":"28","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"file":[{"checksum":"4589234fdb12b4ad72273b311723a7b4","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:37:53Z","relation":"main_file","embargo":"2021-02-28","file_id":"7538","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_size":9646346,"content_type":"application/pdf","creator":"pbhandari","access_level":"open_access","file_name":"Pradeep Bhandari Thesis.pdf"},{"relation":"source_file","file_id":"7539","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","checksum":"aa79490553ca0a5c9b6fbcd152e93928","date_created":"2020-02-28T08:47:14Z","date_updated":"2021-03-01T23:30:04Z","access_level":"closed","embargo_to":"open_access","file_name":"Pradeep Bhandari Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":35252164,"creator":"pbhandari"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7525","abstract":[{"lang":"eng","text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"month":"10","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-011-4"]},"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8657","oa":1,"file_date_updated":"2021-10-07T22:30:03Z","date_created":"2020-10-13T16:46:14Z","date_updated":"2023-09-07T13:20:48Z","author":[{"first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"}],"related_material":{"record":[{"id":"7673","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8250"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"year":"2020","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","day":"14","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-10-14T00:00:00Z","page":"271","citation":{"mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020."},"abstract":[{"text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"main_file","file_id":"8663","embargo":"2021-10-06","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","date_updated":"2021-10-07T22:30:03Z","date_created":"2020-10-15T06:41:20Z","access_level":"open_access","file_name":"kavcicB_thesis202009.pdf","file_size":52636162,"content_type":"application/pdf","creator":"bkavcic"},{"access_level":"closed","file_name":"2020b.zip","embargo_to":"open_access","creator":"bkavcic","content_type":"application/zip","file_size":321681247,"file_id":"8664","relation":"source_file","checksum":"bb35f2352a04db19164da609f00501f3","date_created":"2020-10-15T06:41:53Z","date_updated":"2021-10-07T22:30:03Z"}],"oa_version":"Published Version","status":"public","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","ddc":["571","530","570"],"_id":"8657","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_identifier":{"issn":["2663-337X"]},"month":"10","project":[{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807","name":"Neural stem cells in autism and epilepsy"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"doi":"10.15479/AT:ISTA:8620","file_date_updated":"2021-10-16T22:30:04Z","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","date_updated":"2023-09-07T13:22:14Z","date_created":"2020-10-07T14:53:13Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7800"},{"status":"public","relation":"part_of_dissertation","id":"8131"}]},"author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"}],"has_accepted_license":"1","article_processing_charge":"No","day":"12","page":"138","citation":{"chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.","mla":"Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","apa":"Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620"},"date_published":"2020-10-12T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages.","lang":"eng"}],"ddc":["610"],"status":"public","title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","_id":"8620","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":16155786,"creator":"jmorande","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","access_level":"open_access","date_created":"2020-10-07T14:41:49Z","date_updated":"2021-10-16T22:30:04Z","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","relation":"main_file","file_id":"8621","embargo":"2021-10-15"},{"checksum":"5e0464af453734210ce7aab7b4a92e3a","date_created":"2020-10-07T14:45:07Z","date_updated":"2021-10-16T22:30:04Z","relation":"source_file","file_id":"8622","file_size":24344152,"content_type":"application/x-zip-compressed","creator":"jmorande","access_level":"closed","embargo_to":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.zip"}]},{"oa_version":"None","file":[{"file_name":"ThesisFull20200908.docx","embargo_to":"open_access","access_level":"closed","creator":"dkampjut","file_size":166146359,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8345","relation":"source_file","date_updated":"2021-09-11T22:30:04Z","date_created":"2020-09-08T13:32:06Z","checksum":"dd270baf82121eb4472ad19d77bf227c"},{"creator":"dernst","file_size":13873769,"content_type":"application/pdf","file_name":"2020_Thesis_Kampjut.pdf","access_level":"open_access","date_created":"2020-09-14T15:02:20Z","date_updated":"2021-09-11T22:30:04Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","file_id":"8393","embargo":"2021-09-10","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8340","ddc":["572"],"status":"public","title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","abstract":[{"text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-09T00:00:00Z","citation":{"ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340","apa":"Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","mla":"Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.","chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340."},"page":"242","article_processing_charge":"No","has_accepted_license":"1","day":"09","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6848"}]},"author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut"}],"date_created":"2020-09-07T18:42:23Z","date_updated":"2023-09-07T13:26:17Z","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LeSa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2021-09-11T22:30:04Z","doi":"10.15479/AT:ISTA:8340","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD","oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_identifier":{"isbn":["978-3-99078-008-4"],"issn":["2663-337X"]},"month":"09"},{"date_published":"2020-12-30T00:00:00Z","page":"141","citation":{"ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","apa":"Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983."},"day":"30","has_accepted_license":"1","article_processing_charge":"No","file":[{"checksum":"ec2797ab7a6f253b35df0572b36d1b43","date_created":"2020-12-30T15:34:01Z","date_updated":"2021-12-31T23:30:04Z","embargo":"2021-12-30","file_id":"8984","relation":"main_file","creator":"semtenan","file_size":10848175,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf"},{"access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","file_size":10073648,"content_type":"application/pdf","creator":"semtenan","relation":"source_file","file_id":"8985","checksum":"cc30e6608a9815414024cf548dff3b3a","date_created":"2020-12-30T15:37:36Z","date_updated":"2021-12-31T23:30:04Z"}],"oa_version":"Published Version","ddc":["570"],"title":"Metabolic regulation of Drosophila macrophage tissue invasion","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8983","abstract":[{"lang":"eng","text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8983","oa":1,"month":"12","publication_identifier":{"issn":["2663-337X"]},"date_created":"2020-12-30T15:41:26Z","date_updated":"2023-09-07T13:24:17Z","author":[{"full_name":"Emtenani, Shamsi","first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938"}],"related_material":{"record":[{"id":"8557","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6187"}]},"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","year":"2020","file_date_updated":"2021-12-31T23:30:04Z"},{"day":"13","article_processing_charge":"No","has_accepted_license":"1","citation":{"apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258."},"page":"174","date_published":"2020-01-13T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.","lang":"eng"}],"_id":"7258","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["532"],"status":"public","title":"New approaches to reduce friction in turbulent pipe flow","file":[{"access_level":"closed","file_name":"2020_Scarselli_Thesis.zip","embargo_to":"open_access","creator":"dscarsel","file_size":26640830,"content_type":"application/zip","file_id":"7259","relation":"source_file","checksum":"4df1ab24e9896635106adde5a54615bf","date_updated":"2021-01-13T23:30:05Z","date_created":"2020-01-12T15:57:14Z"},{"content_type":"application/pdf","file_size":8515844,"creator":"dscarsel","access_level":"open_access","file_name":"2020_Scarselli_Thesis.pdf","checksum":"48659ab98e3414293c7a721385c2fd1c","date_created":"2020-01-12T15:56:14Z","date_updated":"2021-01-13T23:30:05Z","relation":"main_file","embargo":"2021-01-12","file_id":"7260"}],"oa_version":"None","month":"01","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines"},{"name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","_id":"25136C54-B435-11E9-9278-68D0E5697425","grant_number":"HO 4393/1-2"}],"doi":"10.15479/AT:ISTA:7258","supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"file_date_updated":"2021-01-13T23:30:05Z","ec_funded":1,"year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BjHo"}],"author":[{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6228"},{"id":"6486","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"id":"422","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-15T12:20:08Z","date_created":"2020-01-12T16:07:26Z"},{"day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"date_published":"2020-10-13T00:00:00Z","page":"117","citation":{"chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653"},"abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","checksum":"c01d9f59794b4b70528f37637c17ad02","file_id":"8666","relation":"source_file","creator":"itomanek","file_size":25131884,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_ITomanek_final_201016.docx","embargo_to":"open_access","access_level":"closed"},{"access_level":"open_access","file_name":"Thesis_ITomanek_final_201016.pdf","file_size":15405675,"content_type":"application/pdf","creator":"itomanek","relation":"main_file","embargo":"2021-10-19","file_id":"8667","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-16T12:14:21Z"}],"oa_version":"Published Version","ddc":["576"],"title":"The evolution of gene expression by copy number and point mutations","status":"public","_id":"8653","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8653","oa":1,"file_date_updated":"2021-10-20T22:30:03Z","date_created":"2020-10-13T13:02:33Z","date_updated":"2023-09-07T13:22:42Z","author":[{"last_name":"Tomanek","first_name":"Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella"}],"related_material":{"record":[{"id":"7652","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","year":"2020"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7427"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"191"},{"id":"449","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub"}],"date_created":"2020-12-01T12:38:18Z","date_updated":"2023-09-19T10:39:33Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","file_date_updated":"2021-12-08T23:30:03Z","doi":"10.15479/AT:ISTA:8822","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12","oa_version":"Published Version","file":[{"file_id":"8919","relation":"source_file","checksum":"210a9675af5e4c78b0b56d920ac82866","date_created":"2020-12-04T07:27:52Z","date_updated":"2021-07-16T22:30:03Z","access_level":"closed","file_name":"Jakub Hajný IST Austria final_JH.docx","embargo_to":"open_access","creator":"jhajny","file_size":91279806,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","file_size":68707697,"creator":"jhajny","access_level":"open_access","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","checksum":"1781385b4aa73eba89cc76c6172f71d2","date_created":"2020-12-09T15:04:41Z","date_updated":"2021-12-08T23:30:03Z","relation":"main_file","file_id":"8933","embargo":"2021-12-07"}],"_id":"8822","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","status":"public","ddc":["580"],"abstract":[{"text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-12-01T00:00:00Z","citation":{"chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822"},"page":"249","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"oa_version":"None","file":[{"access_level":"closed","file_name":"Shayan-Thesis-Final.docx","embargo_to":"open_access","creator":"sshamip","file_size":65194814,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8351","relation":"source_file","checksum":"6e47871c74f85008b9876112eb3fcfa1","date_created":"2020-09-09T11:06:27Z","date_updated":"2021-09-11T22:30:05Z"},{"embargo":"2021-09-10","file_id":"8352","relation":"main_file","date_created":"2020-09-09T11:06:13Z","date_updated":"2021-09-11T22:30:05Z","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","file_name":"Shayan-Thesis-Final.pdf","access_level":"open_access","creator":"sshamip","file_size":23729605,"content_type":"application/pdf"}],"ddc":["570"],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","status":"public","_id":"8350","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-09-09T00:00:00Z","page":"107","citation":{"mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020."},"day":"09","article_processing_charge":"No","has_accepted_license":"1","date_created":"2020-09-09T11:12:10Z","date_updated":"2023-09-27T14:16:45Z","author":[{"full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"661"},{"id":"6508","relation":"part_of_dissertation","status":"public"},{"id":"7001","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"publication_status":"published","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","year":"2020","file_date_updated":"2021-09-11T22:30:05Z","degree_awarded":"PhD","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8350","oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]}},{"has_accepted_license":"1","article_processing_charge":"No","day":"05","citation":{"ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902."},"page":"214","date_published":"2020-06-05T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"_id":"7902","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Genetic dissection of neural development in health and disease at single cell resolution","ddc":["570"],"file":[{"access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_Contreras.docx","file_size":53134142,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"xcontreras","relation":"source_file","file_id":"7927","checksum":"43c172bf006c95b65992d473c7240d13","date_created":"2020-06-05T08:18:08Z","date_updated":"2021-06-07T22:30:03Z"},{"file_name":"PhDThesis_Contreras.pdf","access_level":"open_access","creator":"xcontreras","file_size":35117191,"content_type":"application/pdf","embargo":"2021-06-06","file_id":"7928","relation":"main_file","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z","checksum":"addfed9128271be05cae3608e03a6ec0"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"month":"06","oa":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:7902","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"6830","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"28"},{"status":"public","relation":"dissertation_contains","id":"7815"}]},"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena"}],"date_updated":"2023-10-18T08:45:16Z","date_created":"2020-05-29T08:27:32Z"},{"citation":{"ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","apa":"Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7186.","mla":"Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7186.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019."},"page":"107","date_published":"2019-12-16T00:00:00Z","day":"16","has_accepted_license":"1","article_processing_charge":"No","_id":"7186","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"7194","checksum":"585583c1c875c5d9525703a539668a7c","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-19T15:18:11Z","access_level":"closed","file_name":"DocumentSourceFiles.zip","file_size":19431292,"content_type":"application/zip","creator":"cschwayer"},{"access_level":"open_access","file_name":"Thesis_CS_final.pdf","file_size":19226428,"content_type":"application/pdf","creator":"cschwayer","relation":"main_file","file_id":"7195","checksum":"9b9b24351514948d27cec659e632e2cd","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-19T15:19:21Z"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing."}],"oa":1,"doi":"10.15479/AT:ISTA:7186","degree_awarded":"PhD","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["2663-337X"]},"year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"author":[{"first_name":"Cornelia","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia"}],"related_material":{"record":[{"id":"1096","relation":"dissertation_contains","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7001"}]},"date_created":"2019-12-16T14:26:14Z","date_updated":"2023-09-07T12:56:42Z","file_date_updated":"2020-07-14T12:47:52Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6681","month":"08","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_updated":"2023-09-07T13:10:36Z","date_created":"2019-07-26T11:14:34Z","author":[{"full_name":"Zhechev, Stephan Y","last_name":"Zhechev","first_name":"Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6774"}]},"file_date_updated":"2020-07-14T12:47:37Z","page":"104","citation":{"short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","apa":"Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria."},"date_published":"2019-08-08T00:00:00Z","day":"08","has_accepted_license":"1","article_processing_charge":"No","ddc":["514"],"title":"Algorithmic aspects of homotopy theory and embeddability","status":"public","_id":"6681","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_id":"6771","relation":"main_file","checksum":"3231e7cbfca3b5687366f84f0a57a0c0","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-08-07T13:02:50Z","access_level":"open_access","file_name":"Stephan_Zhechev_thesis.pdf","creator":"szhechev","content_type":"application/pdf","file_size":1464227},{"content_type":"application/octet-stream","file_size":303988,"creator":"szhechev","file_name":"Stephan_Zhechev_thesis.tex","access_level":"closed","date_created":"2019-08-07T13:03:22Z","date_updated":"2020-07-14T12:47:37Z","checksum":"85d65eb27b4377a9e332ee37a70f08b6","relation":"source_file","file_id":"6772"},{"relation":"supplementary_material","file_id":"6773","checksum":"86b374d264ca2dd53e712728e253ee75","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-08-07T13:03:34Z","access_level":"closed","file_name":"supplementary_material.zip","file_size":1087004,"content_type":"application/zip","creator":"szhechev"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."}]},{"file_date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","related_material":{"record":[{"id":"1576","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6900"},{"relation":"dissertation_contains","status":"public","id":"281"},{"id":"2016","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["2663-337X"]},"month":"05","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"doi":"10.15479/AT:ISTA:6473","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","checksum":"75f9184c1346e10a5de5f9cc7338309a","relation":"source_file","file_id":"6480","content_type":"application/zip","file_size":23937464,"creator":"scepeda","file_name":"Thesis_Cepeda.zip","access_level":"closed"},{"content_type":"application/pdf","file_size":16646985,"creator":"scepeda","access_level":"open_access","file_name":"CepedaThesis.pdf","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","date_created":"2019-05-23T11:18:13Z","date_updated":"2020-07-14T12:47:31Z","relation":"main_file","file_id":"6481"}],"oa_version":"Published Version","status":"public","ddc":["004"],"title":"Estimating information flow in single cells","_id":"6473","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"23","keyword":["Information estimation","Time-series","data analysis"],"date_published":"2019-05-23T00:00:00Z","page":"135","citation":{"ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473","apa":"Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473."}},{"page":"189","citation":{"short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria."},"date_published":"2019-03-11T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"11","status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","ddc":["576"],"_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"rprizak","file_size":20995465,"content_type":"application/pdf","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z","checksum":"e60a72de35d270b31f1a23d50f224ec0","file_id":"6072","relation":"main_file"},{"file_name":"thesis_v2_merge.zip","access_level":"closed","content_type":"application/zip","file_size":85705272,"creator":"rprizak","relation":"source_file","title":"Latex files","file_id":"6073","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z","checksum":"67c2630333d05ebafef5f018863a8465"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"doi":"10.15479/at:ista:th6071","publication_identifier":{"issn":["2663-337X"]},"month":"03","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","year":"2019","date_created":"2019-03-06T16:16:10Z","date_updated":"2023-09-22T10:00:48Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1358"},{"id":"955","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:18Z"},{"date_published":"2019-03-18T00:00:00Z","citation":{"ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","apa":"Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.","mla":"Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019."},"page":"375","day":"18","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z","checksum":"6926f66f28079a81c4937e3764be00fc","file_id":"6180","relation":"source_file","creator":"dernst","content_type":"application/x-gzip","file_size":7104482,"file_name":"2019_Schroeder_Thesis.tar.gz","access_level":"closed"},{"creator":"dernst","content_type":"application/pdf","file_size":4228794,"access_level":"open_access","file_name":"2019_Schroeder_Thesis.pdf","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","date_created":"2019-03-28T08:53:52Z","date_updated":"2020-07-14T12:47:21Z","file_id":"6181","relation":"main_file"}],"_id":"6179","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"From Dyson to Pearcey: Universal statistics in random matrix theory","ddc":["515","519"],"status":"public","abstract":[{"text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th6179","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1144","status":"public","relation":"part_of_dissertation"},{"id":"6186","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6185"},{"status":"public","relation":"part_of_dissertation","id":"6182"},{"status":"public","relation":"part_of_dissertation","id":"1012"},{"relation":"part_of_dissertation","status":"public","id":"6184"}]},"date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T08:58:59Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:47:21Z","ec_funded":1},{"type":"dissertation","alternative_title":["IST Austria Thesis"],"abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes. \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6392","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","status":"public","ddc":["570"],"file":[{"access_level":"closed","file_name":"Thesis_Draft_v3.4Final.docx","embargo_to":"open_access","creator":"mlukacisin","file_size":43740796,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6409","relation":"hidden","checksum":"829bda074444857c7935171237bb7c0c","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-10T13:51:49Z"},{"relation":"main_file","embargo":"2020-04-17","file_id":"6410","date_created":"2019-05-10T14:13:42Z","date_updated":"2021-02-11T11:17:16Z","checksum":"56cb5e97f5f8fc41692401b53832d8e0","file_name":"Thesis_Draft_v3.4FinalA.pdf","access_level":"open_access","content_type":"application/pdf","file_size":35228388,"creator":"mlukacisin"}],"oa_version":"Published Version","has_accepted_license":"1","day":"09","citation":{"short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392","apa":"Lukacisin, M. (2019). Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria."},"page":"103","date_published":"2019-05-09T00:00:00Z","file_date_updated":"2021-02-11T11:17:16Z","extern":"1","year":"2019","department":[{"_id":"ToBo"}],"publisher":"IST Austria","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1029"}]},"author":[{"full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin"}],"date_created":"2019-05-09T19:53:00Z","date_updated":"2023-09-22T09:19:41Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"month":"05","oa":1,"doi":"10.15479/AT:ISTA:6392","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}]},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"ddc":["570","006","578","592"],"status":"public","title":"Collective defenses of garden ants against a fungal pathogen","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6435","file":[{"access_level":"open_access","file_name":"tesisDoctoradoBC.pdf","creator":"casillas","content_type":"application/pdf","file_size":3895187,"file_id":"6438","embargo":"2020-05-08","relation":"main_file","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","date_updated":"2021-02-11T11:17:15Z","date_created":"2019-05-13T09:16:20Z"},{"relation":"source_file","file_id":"6439","date_created":"2019-05-13T09:16:20Z","date_updated":"2020-07-14T12:47:30Z","checksum":"3d221aaff7559a7060230a1ff610594f","embargo_to":"open_access","file_name":"tesisDoctoradoBC.zip","access_level":"closed","content_type":"application/zip","file_size":7365118,"creator":"casillas"}],"oa_version":"Published Version","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"day":"07","article_processing_charge":"No","has_accepted_license":"1","page":"183","citation":{"ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.","mla":"Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019."},"date_published":"2019-05-07T00:00:00Z","file_date_updated":"2021-02-11T11:17:15Z","ec_funded":1,"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_updated":"2023-09-07T12:57:04Z","date_created":"2019-05-13T08:58:35Z","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1999"}]},"month":"05","publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"supervisor":[{"last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6435"},{"day":"04","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-02-04T00:00:00Z","page":"138","citation":{"chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075"},"abstract":[{"lang":"eng","text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published 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endocytosis, post-endocytic trafficking and their regulatory controls in plants ","ddc":["575"],"status":"public","_id":"6269","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"02","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:th1075","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2021-02-11T23:30:15Z","date_updated":"2023-09-08T11:43:03Z","date_created":"2019-04-09T14:37:06Z","author":[{"full_name":"Narasimhan, 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Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","apa":"Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","mla":"Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947."},"page":"142","abstract":[{"lang":"eng","text":"Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"6990","relation":"source_file","date_created":"2019-11-06T12:30:02Z","date_updated":"2020-11-07T23:30:03Z","checksum":"53a739752a500f84d0f8ec953cbbd0b6","file_name":"PhDthesis_FrankAssen_revised2.docx","embargo_to":"open_access","access_level":"closed","creator":"fassen","file_size":214172667,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","embargo":"2020-11-06","file_id":"6991","checksum":"8c156b65d9347bb599623a4b09f15d15","date_created":"2019-11-06T12:30:57Z","date_updated":"2020-11-07T23:30:03Z","access_level":"open_access","file_name":"PhDthesis_FrankAssen_revised2.pdf","file_size":83637532,"content_type":"application/pdf","creator":"fassen"}],"oa_version":"Published Version","_id":"6947","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","status":"public","month":"10","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6947","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-11-07T23:30:03Z","author":[{"full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"664"},{"id":"402","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-10-14T16:54:52Z","date_updated":"2023-09-13T08:50:57Z","year":"2019","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria"},{"ddc":["570"],"status":"public","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6849","file":[{"file_id":"6865","relation":"source_file","checksum":"244dc4f74dbfc94f414156092298831f","date_created":"2019-09-09T13:09:45Z","date_updated":"2021-02-10T23:30:09Z","access_level":"closed","file_name":"Thesis_Damaris_Rangel_source.docx","embargo_to":"open_access","creator":"drangel","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18253100},{"request_a_copy":0,"content_type":"application/pdf","file_size":2160109,"creator":"drangel","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","access_level":"open_access","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z","checksum":"59c73be40eeaa1c4db24067270151555","relation":"main_file","embargo":"2020-09-10","file_id":"6866"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. "}],"page":"97","citation":{"ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849."},"date_published":"2019-09-09T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"09","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2019","date_updated":"2023-09-19T10:01:12Z","date_created":"2019-09-06T06:54:16Z","related_material":{"record":[{"id":"5914","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K"}],"file_date_updated":"2021-02-10T23:30:09Z","oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"degree_awarded":"PhD","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"doi":"10.15479/AT:ISTA:6849","publication_identifier":{"issn":["2663-337X"],"isbn":["9783990780039"]},"month":"09"},{"date_updated":"2024-03-28T23:30:21Z","date_created":"2019-11-27T09:07:14Z","author":[{"full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine"}],"related_material":{"record":[{"id":"6266","relation":"old_edition","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"year":"2019","file_date_updated":"2020-07-14T12:47:50Z","degree_awarded":"PhD","supervisor":[{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:7132","oa":1,"month":"06","publication_identifier":{"issn":["2663-337X"]},"file":[{"file_size":5054633,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","access_level":"closed","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:06:10Z","checksum":"34d0fe0f6e0af97b5937205a3e350423","relation":"source_file","file_id":"7133"},{"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","access_level":"open_access","file_size":3231837,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7134","date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","checksum":"140dfb5e3df7edca34f4b6fcc55d876f"}],"oa_version":"Published Version","ddc":["571","573"],"status":"public","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","_id":"7132","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2019-06-27T00:00:00Z","page":"95","citation":{"mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019."},"day":"27","has_accepted_license":"1","article_processing_charge":"No"},{"file_date_updated":"2020-09-15T22:30:05Z","year":"2019","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","last_name":"Käfer"}],"related_material":{"record":[{"id":"5949","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-08-21T15:00:57Z","date_updated":"2023-09-07T13:01:42Z","month":"08","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:6825","supervisor":[{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6825","status":"public","ddc":["570"],"title":"The hippocampus and medial prefrontal cortex during flexible behavior","file":[{"relation":"main_file","file_id":"6846","embargo":"2020-09-05","checksum":"2664420e332a33338568f4f3bfc59287","date_updated":"2020-09-06T22:30:03Z","date_created":"2019-09-03T08:07:13Z","access_level":"open_access","file_name":"Thesis_Kaefer_PDFA.pdf","content_type":"application/pdf","file_size":3205202,"request_a_copy":0,"creator":"kkaefer"},{"embargo_to":"open_access","file_name":"Thesis_Kaefer.zip","access_level":"closed","content_type":"application/zip","file_size":2506835,"creator":"kkaefer","relation":"main_file","file_id":"6847","date_created":"2019-09-03T08:07:17Z","date_updated":"2020-09-15T22:30:05Z","checksum":"9a154eab6f07aa590a3d2651dc0d926a"}],"oa_version":"Published Version","day":"24","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","mla":"Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","apa":"Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825"},"page":"89","date_published":"2019-08-24T00:00:00Z"},{"day":"07","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-06-07T00:00:00Z","page":"141","citation":{"chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","mla":"Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.","apa":"Valosková, K. (2019). The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546"},"abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6549","checksum":"68949c2d96210b45b981a23e9c9cd93c","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-07T13:00:04Z","access_level":"closed","embargo_to":"open_access","file_name":"Katarina Valoskova_PhD thesis_final version.docx","file_size":14110626,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"khribikova"},{"checksum":"555329cd76e196c96f5278c480ee2e6e","date_created":"2019-06-07T13:00:08Z","date_updated":"2021-02-11T11:17:14Z","file_id":"6550","embargo":"2020-06-07","relation":"main_file","creator":"khribikova","file_size":10054156,"content_type":"application/pdf","access_level":"open_access","file_name":"Katarina Valoskova_PhD thesis_final version.pdf"}],"title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","ddc":["570"],"status":"public","_id":"6546","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"acknowledged_ssus":[{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6546","project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2021-02-11T11:17:14Z","date_created":"2019-06-07T12:49:19Z","date_updated":"2023-09-19T10:15:54Z","author":[{"last_name":"Valosková","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","full_name":"Valosková, Katarina"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6187"},{"id":"544","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","year":"2019"},{"abstract":[{"text":"Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a \"winner\" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2020-05-09","file_id":"6389","date_created":"2019-05-07T16:00:39Z","date_updated":"2021-02-11T11:17:15Z","checksum":"77c6c05cfe8b58c8abcf1b854375d084","file_name":"Espinozathesis_all2.pdf","access_level":"open_access","file_size":13966891,"content_type":"application/pdf","creator":"cespinoza"},{"file_size":11159900,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cespinoza","embargo_to":"open_access","file_name":"Espinoza_Thesis.docx","access_level":"closed","date_created":"2019-05-07T16:00:48Z","date_updated":"2020-07-14T12:47:28Z","checksum":"f6aa819f127691a2b0fc21c76eb09746","relation":"source_file","file_id":"6390"}],"status":"public","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","ddc":["570"],"_id":"6363","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"30","date_published":"2019-04-30T00:00:00Z","page":"140","citation":{"ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","apa":"Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6363","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","mla":"Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6363.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363."},"file_date_updated":"2021-02-11T11:17:15Z","date_created":"2019-04-30T11:56:10Z","date_updated":"2023-09-15T12:03:48Z","related_material":{"record":[{"id":"21","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez"}],"department":[{"_id":"PeJo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2019","publication_identifier":{"isbn":["978-3-99078-000-8"],"issn":["2663-337X"]},"month":"04","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:6363","oa":1},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","ddc":["576","579"],"status":"public","_id":"6371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","creator":"cigler","file_size":12597663,"content_type":"application/pdf","embargo":"2020-05-02","file_id":"6373","relation":"main_file","checksum":"c0085d47c58c9cbcab1b0a783480f6da","date_updated":"2021-02-11T11:17:13Z","date_created":"2019-05-03T11:54:52Z"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":34644426,"creator":"cigler","access_level":"closed","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","date_created":"2019-05-03T11:54:54Z","date_updated":"2020-07-14T12:47:28Z","relation":"source_file","file_id":"6374"}],"keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"has_accepted_license":"1","article_processing_charge":"No","day":"03","page":"152","citation":{"chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371"},"date_published":"2019-05-03T00:00:00Z","file_date_updated":"2021-02-11T11:17:13Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"publication_status":"published","year":"2019","date_created":"2019-05-03T11:55:51Z","date_updated":"2024-02-21T13:45:52Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"67"},{"id":"5585","relation":"popular_science","status":"public"}]},"author":[{"first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"doi":"10.15479/AT:ISTA:6371"}]