[{"file_date_updated":"2018-12-12T10:13:02Z","type":"dissertation","oa":1,"doi":"10.15479/AT:ISTA:th_640","has_accepted_license":"1","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","department":[{"_id":"ChWo"}],"citation":{"mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","apa":"Bojsen-Hansen, M. (2016). <i>Tracking, correcting and absorbing water surface waves</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"article_processing_charge":"No","day":"15","date_published":"2016-07-15T00:00:00Z","OA_place":"publisher","abstract":[{"lang":"eng","text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed."}],"publist_id":"6238","page":"114","year":"2016","related_material":{"record":[{"status":"public","id":"5558","relation":"other"}]},"date_created":"2018-12-11T11:50:16Z","oa_version":"Published Version","_id":"1122","language":[{"iso":"eng"}],"title":"Tracking, correcting and absorbing water surface waves","status":"public","file":[{"creator":"system","file_id":"4982","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","file_size":13869345,"date_created":"2018-12-12T10:13:02Z","date_updated":"2018-12-12T10:13:02Z"}],"ddc":["004","005","006","532","621"],"date_updated":"2026-04-08T14:24:06Z","publication_status":"published","month":"07","author":[{"orcid":"0000-0002-4417-3224","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}]},{"ddc":["500"],"date_updated":"2026-04-08T14:24:23Z","publication_status":"published","month":"08","author":[{"full_name":"Mabillard, Isaac","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard"}],"_id":"1123","language":[{"iso":"eng"}],"title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","status":"public","file":[{"file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file","creator":"dernst","file_id":"6809","date_updated":"2019-08-13T08:45:27Z","date_created":"2019-08-13T08:45:27Z","file_size":2227916,"checksum":"2d140cc924cd1b764544906fc22684ef"},{"checksum":"2d140cc924cd1b764544906fc22684ef","file_size":2227916,"success":1,"date_created":"2021-02-22T11:36:34Z","date_updated":"2021-02-22T11:36:34Z","creator":"dernst","file_id":"9178","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2016_Mabillard_Thesis.pdf"}],"related_material":{"record":[{"id":"2159","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-11T11:50:16Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems  in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K  can be mapped into Rd  without triple, quadruple, or, more generally, r-fold points  (image points with at least r  distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd  that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint  simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction  for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK  = (r ≥ 1)k  and d  = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign  can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN  to Rd  without r-Tverberg points when r not a prime power  and\r\nN  = (d  + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K  = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle&quot; and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r  + 1 and r  not a prime power, by a reduction1  to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r  not a prime power.     "}],"publist_id":"6237","page":"55","year":"2016","day":"01","date_published":"2016-08-01T00:00:00Z","OA_place":"publisher","citation":{"mla":"Mabillard, Isaac. <i>Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture</i>. Institute of Science and Technology Austria, 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). <i>Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture</i>. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016."},"department":[{"_id":"UlWa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli"}],"has_accepted_license":"1","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","corr_author":"1","file_date_updated":"2021-02-22T11:36:34Z","type":"dissertation","oa":1},{"month":"08","author":[{"last_name":"Rieckh","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","first_name":"Georg"}],"publication_status":"published","date_updated":"2026-04-08T14:24:58Z","ddc":["570"],"status":"public","file":[{"date_created":"2019-08-13T11:46:25Z","date_updated":"2019-08-13T11:46:25Z","checksum":"ec453918c3bf8e6f460fd1156ef7b493","file_size":2614660,"relation":"main_file","content_type":"application/pdf","access_level":"closed","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","file_id":"6815","creator":"dernst"},{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Georg_Rieckh.pdf","file_id":"8542","creator":"dernst","date_created":"2020-09-21T11:30:40Z","success":1,"date_updated":"2020-09-21T11:30:40Z","checksum":"51ae398166370d18fd22478b6365c4da","file_size":6096178}],"title":"Studying the complexities of transcriptional regulation","language":[{"iso":"eng"}],"_id":"1128","oa_version":"Published Version","date_created":"2018-12-11T11:50:18Z","year":"2016","page":"114","publist_id":"6232","abstract":[{"lang":"eng","text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems."}],"OA_place":"publisher","date_published":"2016-08-01T00:00:00Z","day":"01","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"citation":{"ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","has_accepted_license":"1","oa":1,"type":"dissertation","file_date_updated":"2020-09-21T11:30:40Z"},{"type":"dissertation","file_date_updated":"2021-02-22T11:42:06Z","oa":1,"has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","mla":"Morri, Maurizio. <i>Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors</i>. Institute of Science and Technology Austria, 2016.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"HaJa"}],"supervisor":[{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"01","OA_place":"publisher","date_published":"2016-03-01T00:00:00Z","page":"129","publist_id":"6236","year":"2016","date_created":"2018-12-11T11:50:17Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"1124","file":[{"checksum":"b439803ac0827cdddd56562a54e3b53b","file_size":4785167,"date_updated":"2019-08-13T10:50:00Z","date_created":"2019-08-13T10:50:00Z","creator":"dernst","file_id":"6812","file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file"},{"date_updated":"2021-02-22T11:42:06Z","success":1,"date_created":"2021-02-22T11:42:06Z","file_size":4495669,"checksum":"dd4136247fe472e7d47880ec68ac8de0","file_name":"2016_MORRI_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"9180"}],"status":"public","title":"Optical functionalization of human class A orphan G-protein coupled receptors","publication_status":"published","date_updated":"2026-04-08T14:26:54Z","ddc":["570"],"month":"03","author":[{"last_name":"Morri","id":"4863116E-F248-11E8-B48F-1D18A9856A87","full_name":"Morri, Maurizio","first_name":"Maurizio"}]},{"title":"Theoretical foundations of multi-task lifelong learning","file":[{"creator":"system","file_id":"5056","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":2140062,"date_updated":"2018-12-12T10:14:07Z","date_created":"2018-12-12T10:14:07Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"1126","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","first_name":"Anastasia","full_name":"Pentina, Anastasia"}],"month":"11","date_updated":"2026-04-09T10:49:34Z","publication_status":"published","ddc":["006"],"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"year":"2016","publist_id":"6234","page":"127","abstract":[{"lang":"eng","text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets."}],"ec_funded":1,"oa_version":"Published Version","date_created":"2018-12-11T11:50:17Z","pubrep_id":"776","article_processing_charge":"No","supervisor":[{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","citation":{"ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","mla":"Pentina, Anastasia. <i>Theoretical Foundations of Multi-Task Lifelong Learning</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","apa":"Pentina, A. (2016). <i>Theoretical foundations of multi-task lifelong learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>.","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"ChLa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2016-11-01T00:00:00Z","day":"01","doi":"10.15479/AT:ISTA:TH_776","oa":1,"file_date_updated":"2018-12-12T10:14:07Z","type":"dissertation","corr_author":"1","has_accepted_license":"1","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036."},{"oa":1,"file_date_updated":"2021-02-22T11:51:13Z","type":"dissertation","corr_author":"1","has_accepted_license":"1","acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","supervisor":[{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"JoBo"}],"citation":{"mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016."},"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2016-12-01T00:00:00Z","day":"01","project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"year":"2016","publist_id":"6239","page":"75","ec_funded":1,"abstract":[{"text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments.","lang":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:50:16Z","title":"Selective barriers to horizontal gene transfer","status":"public","file":[{"file_name":"PhDThesis_HandeAcar_1230.pdf","access_level":"closed","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"6814","date_updated":"2019-08-13T11:17:50Z","date_created":"2019-08-13T11:17:50Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_size":3682711},{"file_id":"9184","creator":"dernst","file_name":"2016_Thesis_HandeAcar.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3682711,"checksum":"94bbbc754c36115bf37f8fc11fad43c4","date_updated":"2021-02-22T11:51:13Z","date_created":"2021-02-22T11:51:13Z","success":1}],"language":[{"iso":"eng"}],"_id":"1121","author":[{"last_name":"Acar","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","full_name":"Acar, Hande"}],"month":"12","date_updated":"2026-04-09T10:51:38Z","publication_status":"published","ddc":["570"]},{"_id":"1398","language":[{"iso":"eng"}],"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","file":[{"date_updated":"2025-07-03T06:24:17Z","date_created":"2025-07-03T06:24:17Z","file_size":7590862,"checksum":"f0f7c260e19ec1416824b165afe2d5fd","file_name":"2016_Thesis_Ellis_noSignatures.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"19957"},{"relation":"main_file","access_level":"closed","content_type":"application/pdf","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","file_id":"5106","creator":"system","date_created":"2018-12-12T10:14:51Z","date_updated":"2025-07-03T06:24:39Z","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","file_size":11928241}],"status":"public","ddc":["576"],"date_updated":"2026-04-09T10:52:07Z","publication_status":"published","month":"02","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"publist_id":"5809","page":"130","year":"2016","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"5553"},{"status":"public","id":"5551","relation":"dissertation_contains"},{"status":"public","id":"5552","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:51:47Z","oa_version":"Published Version","citation":{"ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>","mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>"},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"526","article_processing_charge":"No","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"day":"18","date_published":"2016-02-18T00:00:00Z","OA_place":"publisher","file_date_updated":"2025-07-03T06:24:39Z","type":"dissertation","oa":1,"doi":"10.15479/AT:ISTA:TH_526 ","has_accepted_license":"1","acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","corr_author":"1"},{"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"citation":{"mla":"Mishra, Rajiv Kumar. <i>Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus</i>. Institute of Science and Technology Austria, 2016.","ista":"Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria.","ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","apa":"Mishra, R. K. (2016). <i>Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus</i>. Institute of Science and Technology Austria.","chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016.","short":"R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"day":"01","OA_place":"publisher","date_published":"2016-03-01T00:00:00Z","type":"dissertation","file_date_updated":"2021-02-22T11:48:44Z","oa":1,"has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"_id":"1396","status":"public","file":[{"file_name":"Thesis_Mishra_Rajiv (Final).pdf","relation":"main_file","content_type":"application/pdf","access_level":"closed","file_id":"6782","creator":"dernst","date_updated":"2020-07-14T12:44:48Z","date_created":"2019-08-09T12:14:46Z","file_size":2407572,"checksum":"5a010a838faf040f7064f3cfb802f743"},{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2016_RajivMishra_Thesis.pdf","file_id":"9183","creator":"dernst","date_created":"2021-02-22T11:48:44Z","success":1,"date_updated":"2021-02-22T11:48:44Z","checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","file_size":2407572}],"title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","publication_status":"published","date_updated":"2026-04-09T10:52:26Z","ddc":["570"],"month":"03","author":[{"last_name":"Mishra","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","first_name":"Rajiv Kumar","full_name":"Mishra, Rajiv Kumar"}],"page":"83","publist_id":"5811","abstract":[{"text":"CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity.","lang":"eng"}],"year":"2016","related_material":{"record":[{"status":"public","id":"1432","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:51:46Z","oa_version":"Published Version"},{"date_published":"2016-07-07T00:00:00Z","OA_place":"publisher","day":"07","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"citation":{"mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>.","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:1130","main_file_link":[{"url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf","open_access":"1"}],"file_date_updated":"2021-11-17T13:46:55Z","type":"dissertation","month":"07","author":[{"last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","first_name":"Thorsten"}],"ddc":["000"],"date_updated":"2026-04-09T10:54:01Z","publication_status":"published","title":"Automatic synthesis of synchronisation primitives for concurrent programs","file":[{"file_size":1523935,"checksum":"319a506831650327e85376db41fc1094","date_updated":"2021-02-22T11:39:32Z","date_created":"2021-02-22T11:39:32Z","success":1,"creator":"dernst","file_id":"9179","file_name":"2016_Tarrach_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file"},{"access_level":"closed","content_type":"application/pdf","relation":"main_file","file_name":"2016_Tarrach_Thesispdfa.pdf","creator":"cchlebak","file_id":"10296","date_created":"2021-11-16T14:14:38Z","date_updated":"2021-11-17T13:46:55Z","checksum":"39efcd789f0ad859ff15652cb7afc412","file_size":1306068}],"status":"public","_id":"1130","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"2218","relation":"part_of_dissertation"},{"id":"2445","relation":"part_of_dissertation","status":"public"},{"id":"1729","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-11T11:50:19Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"year":"2016","abstract":[{"text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency.","lang":"eng"}],"ec_funded":1,"publist_id":"6230","page":"151"},{"title":"Evolution of transcriptional regulatory sequences","file":[{"file_id":"6810","creator":"dernst","relation":"main_file","access_level":"closed","content_type":"application/pdf","file_name":"Tugrul_thesis_w_signature_page.pdf","checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_size":3695257,"date_created":"2019-08-13T08:53:52Z","date_updated":"2019-08-13T08:53:52Z"},{"file_id":"9182","creator":"dernst","file_name":"2016_Tugrul_Thesis.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"293e388d70563760f6b24c3e66283dda","file_size":3880811,"date_updated":"2021-02-22T11:45:20Z","success":1,"date_created":"2021-02-22T11:45:20Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"1131","month":"07","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","first_name":"Murat","orcid":"0000-0002-8523-0758"}],"date_updated":"2026-04-09T10:52:40Z","publication_status":"published","ddc":["576"],"year":"2016","publist_id":"6229","page":"89","abstract":[{"text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"5554"},{"status":"public","relation":"part_of_dissertation","id":"1666"}]},"date_created":"2018-12-11T11:50:19Z","article_processing_charge":"No","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","citation":{"mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2016-07-01T00:00:00Z","day":"01","oa":1,"file_date_updated":"2021-02-22T11:45:20Z","type":"dissertation","corr_author":"1","has_accepted_license":"1","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me."},{"date_published":"2016-07-01T00:00:00Z","OA_place":"publisher","day":"01","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016."},"department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","oa":1,"file_date_updated":"2021-02-22T13:42:47Z","type":"dissertation","author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"month":"07","ddc":["576"],"date_updated":"2026-04-09T14:25:34Z","publication_status":"published","title":"Evolutionary proccesses in variable emvironments","file":[{"file_id":"6811","creator":"dernst","relation":"main_file","access_level":"closed","content_type":"application/pdf","file_name":"Novak_thesis.pdf","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","file_size":3564901,"date_created":"2019-08-13T09:01:00Z","date_updated":"2019-08-13T09:01:00Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2016_Novak_Thesis.pdf","file_id":"9186","creator":"dernst","date_created":"2021-02-22T13:42:47Z","success":1,"date_updated":"2021-02-22T13:42:47Z","checksum":"30808d2f7ca920e09f63a95cdc49bffd","file_size":2814384}],"status":"public","_id":"1125","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:50:17Z","related_material":{"record":[{"status":"public","id":"2023","relation":"part_of_dissertation"}]},"year":"2016","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"publist_id":"6235","page":"124"},{"day":"01","date_published":"2015-04-01T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>.","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","apa":"Sharmanska, V. (2015). <i>Learning with attributes for object recognition: Parametric and non-parametrics views</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","mla":"Sharmanska, Viktoriia. <i>Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>."},"department":[{"_id":"ChLa"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","has_accepted_license":"1","corr_author":"1","main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"type":"dissertation","file_date_updated":"2021-11-17T13:47:24Z","oa":1,"doi":"10.15479/at:ista:1401","ddc":["000"],"publication_status":"published","date_updated":"2026-04-09T14:25:49Z","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","orcid":"0000-0003-0192-9308"}],"month":"04","_id":"1401","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_id":"9177","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2015_Thesis_Sharmanska.pdf","file_size":7964342,"checksum":"3605b402bb6934e09ae4cf672c84baf7","date_created":"2021-02-22T11:33:17Z","success":1,"date_updated":"2021-02-22T11:33:17Z"},{"date_created":"2021-11-16T14:40:45Z","date_updated":"2021-11-17T13:47:24Z","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","file_size":7372241,"content_type":"application/pdf","access_level":"closed","relation":"main_file","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","creator":"cchlebak","file_id":"10297"}],"status":"public","title":"Learning with attributes for object recognition: Parametric and non-parametrics views","date_created":"2018-12-11T11:51:48Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views."}],"page":"144","publist_id":"5806","year":"2015"},{"year":"2015","abstract":[{"text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease.","lang":"eng"}],"publist_id":"5807","type":"dissertation","page":"183","corr_author":"1","oa_version":"None","related_material":{"record":[{"relation":"part_of_dissertation","id":"2000","status":"public"},{"id":"1709","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"2858"},{"status":"public","id":"2816","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2247"},{"relation":"part_of_dissertation","id":"3260","status":"public"},{"id":"3157","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-11T11:51:48Z","publication_identifier":{"issn":["2663-337X"]},"title":"The subclonal evolution of cancer","supervisor":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"article_processing_charge":"No","status":"public","_id":"1400","citation":{"mla":"Reiter, Johannes. <i>The Subclonal Evolution of Cancer</i>. Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","apa":"Reiter, J. (2015). <i>The subclonal evolution of cancer</i>. Institute of Science and Technology Austria.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"KrCh"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"degree_awarded":"PhD","date_published":"2015-04-01T00:00:00Z","OA_place":"publisher","month":"04","author":[{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"}],"day":"01","date_updated":"2026-04-09T14:26:24Z","publication_status":"published"},{"year":"2015","abstract":[{"text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.","lang":"eng"}],"page":"144","type":"dissertation","publist_id":"5808","oa_version":"None","corr_author":"1","date_created":"2018-12-11T11:51:48Z","related_material":{"record":[{"id":"1662","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1792","status":"public"},{"status":"public","id":"2255","relation":"part_of_dissertation"}]},"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"status":"public","title":"On the approximation of intrinsic volumes","publisher":"Institute of Science and Technology Austria","_id":"1399","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"HeEd"}],"citation":{"short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","apa":"Pausinger, F. (2015). <i>On the approximation of intrinsic volumes</i>. Institute of Science and Technology Austria.","chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","mla":"Pausinger, Florian. <i>On the Approximation of Intrinsic Volumes</i>. Institute of Science and Technology Austria, 2015."},"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2015-06-01T00:00:00Z","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","full_name":"Pausinger, Florian","first_name":"Florian","orcid":"0000-0002-8379-3768"}],"month":"06","OA_place":"publisher","day":"01","publication_status":"published","date_updated":"2026-04-16T10:09:04Z"},{"oa_version":"None","corr_author":"1","date_created":"2018-12-11T11:51:46Z","year":"2014","page":"131","type":"dissertation","publist_id":"5814","abstract":[{"lang":"eng","text":"In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi.  The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants."}],"author":[{"first_name":"Matthias","full_name":"Konrad, Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"}],"month":"02","OA_place":"publisher","date_published":"2014-02-01T00:00:00Z","publication_status":"published","date_updated":"2026-04-09T14:27:01Z","day":"01","status":"public","article_processing_charge":"No","supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","first_name":"Sylvia M"}],"title":"Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","_id":"1395","department":[{"_id":"SyCr"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"M. Konrad, Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus, Institute of Science and Technology Austria, 2014.","ama":"Konrad M. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. 2014.","ieee":"M. Konrad, “Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus,” Institute of Science and Technology Austria, 2014.","chicago":"Konrad, Matthias. “Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus.” Institute of Science and Technology Austria, 2014.","apa":"Konrad, M. (2014). <i>Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus</i>. Institute of Science and Technology Austria.","ista":"Konrad M. 2014. Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus. Institute of Science and Technology Austria.","mla":"Konrad, Matthias. <i>Immune Defences in Ants: Effects of Social Immunisation and a Fungal Ectosymbiont in the Ant Lasius Neglectus</i>. Institute of Science and Technology Austria, 2014."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"date_published":"2014-12-01T00:00:00Z","month":"12","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","full_name":"Marhavá, Petra","first_name":"Petra"}],"OA_place":"publisher","day":"01","publication_status":"published","date_updated":"2026-04-09T14:27:28Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"status":"public","title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","publisher":"Institute of Science and Technology Austria","_id":"1402","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Marhavá, Petra. <i>Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","apa":"Marhavá, P. (2014). <i>Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"JiFr"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa_version":"None","corr_author":"1","date_created":"2018-12-11T11:51:49Z","year":"2014","abstract":[{"text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"page":"90","type":"dissertation","publist_id":"5805"},{"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>","short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","mla":"Zufferey, Damien. <i>Analysis of Dynamic Message Passing Programs</i>. Institute of Science and Technology Austria, 2013, doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>.","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>.","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","apa":"Zufferey, D. (2013). <i>Analysis of dynamic message passing programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria."},"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"day":"05","OA_place":"publisher","date_published":"2013-09-05T00:00:00Z","file_date_updated":"2021-11-17T13:47:58Z","type":"dissertation","main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"doi":"10.15479/at:ista:1405","oa":1,"has_accepted_license":"1","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","corr_author":"1","language":[{"iso":"eng"}],"_id":"1405","title":"Analysis of dynamic message passing programs","status":"public","file":[{"creator":"dernst","file_id":"9176","file_name":"2013_Zufferey_thesis_final.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":1514906,"checksum":"ed2d7b52933d134e8dc69d569baa284e","date_updated":"2021-02-22T11:28:36Z","success":1,"date_created":"2021-02-22T11:28:36Z"},{"date_created":"2021-11-16T14:42:52Z","date_updated":"2021-11-17T13:47:58Z","checksum":"cecc4c4b14225bee973d32e3dba91a55","file_size":1378313,"access_level":"closed","content_type":"application/pdf","relation":"main_file","file_name":"2013_Zufferey_thesis_final_pdfa.pdf","creator":"cchlebak","file_id":"10298"}],"date_updated":"2026-04-09T14:35:24Z","publication_status":"published","ddc":["000"],"month":"09","author":[{"orcid":"0000-0002-3197-8736","first_name":"Damien","full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5802","page":"134","abstract":[{"lang":"eng","text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point."}],"ec_funded":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"year":"2013","related_material":{"record":[{"id":"4361","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"3251","relation":"part_of_dissertation"},{"status":"public","id":"2847","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:51:50Z","oa_version":"Published Version"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"1406","alternative_title":["ISTA Thesis"],"citation":{"short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013."},"department":[{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","status":"public","supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","day":"01","date_updated":"2026-04-09T14:34:43Z","publication_status":"published","date_published":"2013-10-01T00:00:00Z","OA_place":"publisher","author":[{"full_name":"Campinho, Pedro","orcid":"0000-0002-8526-5416","first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87"}],"month":"10","abstract":[{"text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading.","lang":"eng"}],"publist_id":"5801","page":"123","type":"dissertation","year":"2013","date_created":"2018-12-11T11:51:50Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"corr_author":"1","oa_version":"None"},{"date_published":"2012-06-01T00:00:00Z","author":[{"last_name":"Kim","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","first_name":"Sooyun"}],"month":"06","OA_place":"publisher","day":"01","publication_status":"published","date_updated":"2026-04-09T14:36:04Z","publication_identifier":{"issn":["2663-337X"]},"status":"public","supervisor":[{"orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Active properties of hippocampal CA3 pyramidal neuron dendrites","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"_id":"2964","citation":{"short":"S. Kim, Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites, Institute of Science and Technology Austria, 2012.","ama":"Kim S. Active properties of hippocampal CA3 pyramidal neuron dendrites. 2012.","apa":"Kim, S. (2012). <i>Active properties of hippocampal CA3 pyramidal neuron dendrites</i>. Institute of Science and Technology Austria.","ieee":"S. Kim, “Active properties of hippocampal CA3 pyramidal neuron dendrites,” Institute of Science and Technology Austria, 2012.","chicago":"Kim, Sooyun. “Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites.” Institute of Science and Technology Austria, 2012.","ista":"Kim S. 2012. Active properties of hippocampal CA3 pyramidal neuron dendrites. Institute of Science and Technology Austria.","mla":"Kim, Sooyun. <i>Active Properties of Hippocampal CA3 Pyramidal Neuron Dendrites</i>. Institute of Science and Technology Austria, 2012."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"degree_awarded":"PhD","oa_version":"None","corr_author":"1","related_material":{"record":[{"status":"public","id":"3258","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T12:00:35Z","year":"2012","abstract":[{"lang":"eng","text":"CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. These neurons receive multiple excitatory inputs from numerous sources. Therefore, the rules of spatiotemporal integration of multiple synaptic inputs and propagation of action potentials are important to understand how CA3 neurons contribute to higher brain functions at cellular level. By using confocally targeted patch-clamp recording techniques, we investigated the biophysical properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic domains critical for action potential initiation and propagation: In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking synaptic events. These findings can be explained by a high Na+-to-K+ conductance density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently than distal perforant inputs by showing that the distal synapses trigger a different form of activity represented by dendritic spikes. The high probability of dendritic spike initiation in the distal area may enhance the computational power of CA3 pyramidal neurons in the hippocampal network.  "}],"page":"65","type":"dissertation","publist_id":"3755"},{"language":[{"iso":"eng"}],"_id":"3275","file":[{"creator":"dernst","file_id":"6177","file_name":"2011_Thesis_Kathrin_Schumann.pdf","access_level":"closed","content_type":"application/pdf","relation":"main_file","checksum":"e69eee6252660f0b694a2ea8923ddc72","file_size":4487708,"date_updated":"2020-07-14T12:46:06Z","date_created":"2019-03-26T08:12:21Z"},{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2011_Thesis_Schumann_noS.pdf","creator":"dernst","file_id":"9175","success":1,"date_created":"2021-02-22T11:24:30Z","date_updated":"2021-02-22T11:24:30Z","file_size":4313127,"checksum":"71727d63f424b5b446f68f4b87ecadc0"}],"status":"public","title":"The role of chemotactic gradients in dendritic cell migration","publication_status":"published","date_updated":"2026-04-09T14:36:24Z","ddc":["570","579"],"month":"03","author":[{"first_name":"Kathrin","full_name":"Schumann, Kathrin","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","last_name":"Schumann"}],"page":"141","publist_id":"3371","abstract":[{"text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. ","lang":"eng"}],"year":"2011","date_created":"2018-12-11T12:02:24Z","oa_version":"Published Version","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011."},"department":[{"_id":"MiSi"}],"pubrep_id":"11","article_processing_charge":"No","supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"publication_identifier":{"issn":["2663-337X"]},"day":"01","OA_place":"publisher","date_published":"2011-03-01T00:00:00Z","type":"dissertation","file_date_updated":"2021-02-22T11:24:30Z","oa":1,"acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","has_accepted_license":"1","corr_author":"1"}]