[{"type":"dissertation","status":"public","_id":"8983","file_date_updated":"2021-12-31T23:30:04Z","department":[{"_id":"DaSi"}],"date_updated":"2023-09-07T13:24:17Z","supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"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."}],"oa_version":"Published Version","related_material":{"record":[{"id":"8557","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6187"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"ec2797ab7a6f253b35df0572b36d1b43","file_id":"8984","embargo":"2021-12-30","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-12-30T15:34:01Z","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","date_updated":"2021-12-31T23:30:04Z","file_size":10848175,"creator":"semtenan"},{"file_id":"8985","checksum":"cc30e6608a9815414024cf548dff3b3a","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","date_created":"2020-12-30T15:37:36Z","creator":"semtenan","file_size":10073648,"date_updated":"2021-12-31T23:30:04Z"}],"article_processing_charge":"No","author":[{"id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","last_name":"Emtenani","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi"}],"title":"Metabolic regulation of Drosophila macrophage tissue invasion","citation":{"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.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"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.","page":"141","date_created":"2020-12-30T15:41:26Z","doi":"10.15479/AT:ISTA:8983","date_published":"2020-12-30T00:00:00Z","year":"2020","has_accepted_license":"1","day":"30"},{"title":"New approaches to reduce friction in turbulent pipe flow","article_processing_charge":"No","author":[{"first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","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.","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","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","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258"},"project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin"},{"grant_number":"737549","name":"Eliminating turbulence in oil pipelines","_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25136C54-B435-11E9-9278-68D0E5697425","name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","grant_number":"HO 4393/1-2"}],"date_created":"2020-01-12T16:07:26Z","doi":"10.15479/AT:ISTA:7258","date_published":"2020-01-13T00:00:00Z","page":"174","day":"13","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"BjHo"}],"file_date_updated":"2021-01-13T23:30:05Z","ddc":["532"],"date_updated":"2023-09-15T12:20:08Z","supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"status":"public","type":"dissertation","_id":"7258","ec_funded":1,"related_material":{"record":[{"id":"6228","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6486"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"422","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/zip","embargo_to":"open_access","checksum":"4df1ab24e9896635106adde5a54615bf","file_id":"7259","creator":"dscarsel","date_updated":"2021-01-13T23:30:05Z","file_size":26640830,"date_created":"2020-01-12T15:57:14Z","file_name":"2020_Scarselli_Thesis.zip"},{"date_created":"2020-01-12T15:56:14Z","file_name":"2020_Scarselli_Thesis.pdf","date_updated":"2021-01-13T23:30:05Z","file_size":8515844,"creator":"dscarsel","checksum":"48659ab98e3414293c7a721385c2fd1c","file_id":"7260","embargo":"2021-01-12","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"None","abstract":[{"lang":"eng","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."}]},{"_id":"8653","type":"dissertation","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"status":"public","date_updated":"2023-09-07T13:22:42Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"ddc":["576"],"file_date_updated":"2021-10-20T22:30:03Z","department":[{"_id":"CaGu"}],"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"itomanek","date_updated":"2021-10-20T22:30:03Z","file_size":25131884,"date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"8666","checksum":"c01d9f59794b4b70528f37637c17ad02"},{"file_id":"8667","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","embargo":"2021-10-19","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-16T12:14:21Z","file_name":"Thesis_ITomanek_final_201016.pdf","creator":"itomanek","date_updated":"2021-10-20T22:30:03Z","file_size":15405675}],"related_material":{"record":[{"id":"7652","status":"public","relation":"research_data"}]},"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.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","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.","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","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi: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.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"}],"title":"The evolution of gene expression by copy number and point mutations","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"13","page":"117","date_created":"2020-10-13T13:02:33Z","date_published":"2020-10-13T00:00:00Z","doi":"10.15479/AT:ISTA:8653"},{"article_processing_charge":"No","author":[{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"}],"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"249","date_created":"2020-12-01T12:38:18Z","doi":"10.15479/AT:ISTA:8822","date_published":"2020-12-01T00:00:00Z","year":"2020","has_accepted_license":"1","day":"01","type":"dissertation","status":"public","_id":"8822","department":[{"_id":"JiFr"}],"file_date_updated":"2021-12-08T23:30:03Z","date_updated":"2023-09-19T10:39:33Z","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"ddc":["580"],"alternative_title":["ISTA Thesis"],"month":"12","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"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7427","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"status":"public","id":"7500","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"191","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8919","checksum":"210a9675af5e4c78b0b56d920ac82866","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Jakub Hajný IST Austria final_JH.docx","date_created":"2020-12-04T07:27:52Z","file_size":91279806,"date_updated":"2021-07-16T22:30:03Z","creator":"jhajny"},{"date_created":"2020-12-09T15:04:41Z","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","creator":"jhajny","date_updated":"2021-12-08T23:30:03Z","file_size":68707697,"checksum":"1781385b4aa73eba89cc76c6172f71d2","file_id":"8933","embargo":"2021-12-07","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"None","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"related_material":{"record":[{"status":"public","id":"661","relation":"part_of_dissertation"},{"status":"public","id":"6508","relation":"part_of_dissertation"},{"status":"public","id":"7001","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"735"}]},"file":[{"date_created":"2020-09-09T11:06:27Z","file_name":"Shayan-Thesis-Final.docx","date_updated":"2021-09-11T22:30:05Z","file_size":65194814,"creator":"sshamip","file_id":"8351","checksum":"6e47871c74f85008b9876112eb3fcfa1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"},{"creator":"sshamip","file_size":23729605,"date_updated":"2021-09-11T22:30:05Z","file_name":"Shayan-Thesis-Final.pdf","date_created":"2020-09-09T11:06:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2021-09-10","file_id":"8352","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","_id":"8350","file_date_updated":"2021-09-11T22:30:05Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"ddc":["570"],"supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-27T14:16:45Z","publisher":"Institute of Science and Technology Austria","oa":1,"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.","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8350","date_created":"2020-09-09T11:12:10Z","page":"107","day":"09","has_accepted_license":"1","year":"2020","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","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","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.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria."}},{"date_updated":"2023-10-18T08:45:16Z","supervisor":[{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-06-07T22:30:03Z","_id":"7902","type":"dissertation","status":"public","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"43c172bf006c95b65992d473c7240d13","file_id":"7927","date_updated":"2021-06-07T22:30:03Z","file_size":53134142,"creator":"xcontreras","date_created":"2020-06-05T08:18:08Z","file_name":"PhDThesis_Contreras.docx"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"addfed9128271be05cae3608e03a6ec0","file_id":"7928","embargo":"2021-06-06","date_updated":"2021-06-07T22:30:03Z","file_size":35117191,"creator":"xcontreras","date_created":"2020-06-05T08:18:07Z","file_name":"PhDThesis_Contreras.pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6830","status":"public"},{"status":"public","id":"28","relation":"dissertation_contains"},{"id":"7815","status":"public","relation":"dissertation_contains"}]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","citation":{"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","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi: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.","ieee":"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.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","last_name":"Contreras"}],"title":"Genetic dissection of neural development in health and disease at single cell resolution","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"year":"2020","has_accepted_license":"1","day":"05","page":"214","date_created":"2020-05-29T08:27:32Z","doi":"10.15479/AT:ISTA:7902","date_published":"2020-06-05T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria"},{"publisher":"École Polytechnique Fédérale de Lausanne","oa":1,"main_file_link":[{"url":"https://www.doi.org/10.5075/epfl-thesis-7101","open_access":"1"}],"month":"09","abstract":[{"lang":"eng","text":"One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope."}],"oa_version":"Published Version","page":"244","doi":"10.5075/epfl-thesis-7101","date_published":"2019-09-27T00:00:00Z","date_created":"2020-08-27T11:22:24Z","year":"2019","degree_awarded":"PhD","publication_status":"published","day":"27","language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"8311","author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"}],"article_processing_charge":"No","title":"Secure, confidential blockchains providing high throughput and low latency","supervisor":[{"full_name":"Ford, Bryan Alexander","last_name":"Ford","first_name":"Bryan Alexander"}],"citation":{"ista":"Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne.","chicago":"Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101.","ama":"Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101","apa":"Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101","ieee":"E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019.","short":"E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.","mla":"Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101."},"date_updated":"2021-12-20T15:30:47Z","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"day":"24","has_accepted_license":"1","year":"2019","doi":"10.15479/AT:ISTA:6957","date_published":"2019-10-24T00:00:00Z","date_created":"2019-10-22T12:08:43Z","page":"138","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957.","ista":"Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria.","mla":"Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.","apa":"Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957","ama":"Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957","short":"C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019.","ieee":"C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019."},"title":"Onset of turbulence in plane Poiseuille flow","author":[{"full_name":"Paranjape, Chaitanya S","last_name":"Paranjape","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","first_name":"Chaitanya S"}],"article_processing_charge":"No","file":[{"date_created":"2019-10-23T09:54:43Z","file_name":"Chaitanya_Paranjape_source_files_tex_figures.zip","date_updated":"2020-07-14T12:47:46Z","file_size":45828099,"creator":"cparanjape","file_id":"6962","checksum":"7ba298ba0ce7e1d11691af6b8eaf0a0a","content_type":"application/zip","access_level":"closed","relation":"source_file"},{"file_size":19504197,"date_updated":"2020-07-14T12:47:46Z","creator":"cparanjape","file_name":"Chaitanya_Paranjape_Thesis.pdf","date_created":"2019-10-23T10:37:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6963","checksum":"642697618314e31ac31392da7909c2d9"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","oa_version":"Published Version","abstract":[{"text":"In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable. The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent. In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature. Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.","lang":"eng"}],"month":"10","alternative_title":["ISTA Thesis"],"ddc":["532"],"supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"date_updated":"2023-09-07T12:53:25Z","file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"BjHo"}],"_id":"6957","status":"public","keyword":["Instabilities","Turbulence","Nonlinear dynamics"],"type":"dissertation"},{"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2019-12-16T00:00:00Z","doi":"10.15479/AT:ISTA:7186","date_created":"2019-12-16T14:26:14Z","page":"107","day":"16","has_accepted_license":"1","year":"2019","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","author":[{"first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","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.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186","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","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."},"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1096"},{"status":"public","id":"7001","relation":"part_of_dissertation"}]},"file":[{"file_id":"7194","checksum":"585583c1c875c5d9525703a539668a7c","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"DocumentSourceFiles.zip","date_created":"2019-12-19T15:18:11Z","creator":"cschwayer","file_size":19431292,"date_updated":"2020-07-14T12:47:52Z"},{"checksum":"9b9b24351514948d27cec659e632e2cd","file_id":"7195","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-12-19T15:19:21Z","file_name":"Thesis_CS_final.pdf","creator":"cschwayer","date_updated":"2020-07-14T12:47:52Z","file_size":19226428}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"7186","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"CaHe"}],"ddc":["570"],"supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:56:42Z"},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"08","year":"2019","has_accepted_license":"1","date_created":"2019-07-26T11:14:34Z","doi":"10.15479/AT:ISTA:6681","date_published":"2019-08-08T00:00:00Z","page":"104","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 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.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","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","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.","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria."},"title":"Algorithmic aspects of homotopy theory and embeddability","article_processing_charge":"No","author":[{"full_name":"Zhechev, Stephan Y","last_name":"Zhechev","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan Y"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3231e7cbfca3b5687366f84f0a57a0c0","file_id":"6771","date_updated":"2020-07-14T12:47:37Z","file_size":1464227,"creator":"szhechev","date_created":"2019-08-07T13:02:50Z","file_name":"Stephan_Zhechev_thesis.pdf"},{"file_id":"6772","checksum":"85d65eb27b4377a9e332ee37a70f08b6","content_type":"application/octet-stream","access_level":"closed","relation":"source_file","date_created":"2019-08-07T13:03:22Z","file_name":"Stephan_Zhechev_thesis.tex","date_updated":"2020-07-14T12:47:37Z","file_size":303988,"creator":"szhechev"},{"file_name":"supplementary_material.zip","date_created":"2019-08-07T13:03:34Z","file_size":1087004,"date_updated":"2020-07-14T12:47:37Z","creator":"szhechev","checksum":"86b374d264ca2dd53e712728e253ee75","file_id":"6773","content_type":"application/zip","relation":"supplementary_material","access_level":"closed"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"6774","relation":"part_of_dissertation"}]},"_id":"6681","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["514"],"date_updated":"2023-09-07T13:10:36Z","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:37Z"}]