[{"title":"Identification and characterization of novel auxin-cytokinin cross-talk components","OA_place":"publisher","file_date_updated":"2020-12-02T23:30:08Z","degree_awarded":"PhD","related_material":{"record":[{"id":"1024","status":"public","relation":"part_of_dissertation"}]},"citation":{"apa":"Hurny, A. (2018). <i>Identification and characterization of novel auxin-cytokinin cross-talk components</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","mla":"Hurny, Andrej. <i>Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>."},"oa_version":"Published Version","_id":"539","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi_confirm":"1","publication_status":"published","publist_id":"7277","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"pubrep_id":"930","year":"2018","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:47:03Z","author":[{"orcid":"0000-0003-3638-1426","last_name":"Hurny","full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej"}],"file":[{"embargo_to":"open_access","file_name":"2018_Hurny_thesis_source.docx","relation":"source_file","file_id":"6226","access_level":"closed","date_updated":"2020-12-02T23:30:08Z","file_size":28112114,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T09:37:56Z","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","creator":"dernst"},{"file_size":12524427,"content_type":"application/pdf","creator":"dernst","checksum":"ecbe481a1413d270bd501b872c7ed54f","date_created":"2019-04-05T09:37:55Z","relation":"main_file","file_name":"2018_Hurny_thesis.pdf","date_updated":"2020-12-02T09:52:16Z","embargo":"2019-07-10","access_level":"open_access","file_id":"6227"}],"page":"147","supervisor":[{"orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"month":"01","doi":"10.15479/AT:ISTA:th_930","date_updated":"2026-07-29T13:30:01Z","oa":1,"date_published":"2018-01-01T00:00:00Z","article_processing_charge":"No","type":"dissertation","corr_author":"1","ddc":["570"],"abstract":[{"text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth.","lang":"eng"}]},{"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"28","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1027"},{"id":"696","status":"public","relation":"part_of_dissertation"},{"id":"1619","status":"public","relation":"part_of_dissertation"}]},"citation":{"chicago":"Lukacisinova, Marta. “Genetic Determinants of Antibiotic Resistance Evolution.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">https://doi.org/10.15479/AT:ISTA:th1072</a>.","ista":"Lukacisinova M. 2018. Genetic determinants of antibiotic resistance evolution. Institute of Science and Technology Austria.","ieee":"M. Lukacisinova, “Genetic determinants of antibiotic resistance evolution,” Institute of Science and Technology Austria, 2018.","short":"M. Lukacisinova, Genetic Determinants of Antibiotic Resistance Evolution, Institute of Science and Technology Austria, 2018.","mla":"Lukacisinova, Marta. <i>Genetic Determinants of Antibiotic Resistance Evolution</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">10.15479/AT:ISTA:th1072</a>.","apa":"Lukacisinova, M. (2018). <i>Genetic determinants of antibiotic resistance evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">https://doi.org/10.15479/AT:ISTA:th1072</a>","ama":"Lukacisinova M. Genetic determinants of antibiotic resistance evolution. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1072\">10.15479/AT:ISTA:th1072</a>"},"oa_version":"Published Version","_id":"6263","title":"Genetic determinants of antibiotic resistance evolution","OA_place":"publisher","file_date_updated":"2021-02-11T11:17:17Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"LifeSc"}],"degree_awarded":"PhD","type":"dissertation","corr_author":"1","ddc":["570","576","579"],"abstract":[{"lang":"eng","text":"Antibiotic  resistance  can  emerge  spontaneously  through  genomic  mutation  and  render treatment   ineffective.   To   counteract   this process, in   addition   to   the   discovery   and description of resistance mechanisms,a deeper understanding of resistanceevolvabilityand its  determinantsis  needed. To address  this challenge,  this  thesisuncoversnew  genetic determinants   of   resistance   evolvability   using   a   customized   robotic   setup, exploressystematic   ways   in   which   resistance   evolution   is   perturbed   due   to dose-responsecharacteristics  of  drugs and  mutation  rate  differences,and  mathematically  investigates the evolutionary fate of one specific type of evolvability modifier -a stress-induced mutagenesis allele.We  find  severalgenes  which  strongly  inhibit  or  potentiate  resistance  evolution.  In  order to identify   them,   we   first developedan   automated   high-throughput   feedback-controlled protocol whichkeeps the population size and selection pressure approximately constant for hundreds  of  cultures  by  dynamically  re-diluting  the  cultures  and  adjusting  the  antibiotic concentration.  We  implementedthis  protocol  on  a  customized  liquid  handling  robot  and propagated  100  different  gene  deletion  strains  of Escherichia  coliin  triplicate  for  over  100 generations  in  tetracycline  and  in  chloramphenicol,  and  comparedtheir  adaptation  rates.We  find  a  diminishing  returns  pattern,  where  initially  sensitive  strains  adapted  more compared to less sensitive ones.  Our data uncover that deletions of certain genes which do not  affect  mutation  rate,including  efflux  pump  components,  a  chaperone  and severalstructural  and regulatory  genes  can strongly  and  reproducibly  alterresistance  evolution. Sequencing   analysis of   evolved   populations   indicates   that   epistasis   with   resistance mutations  is  the  most  likelyexplanation. This  work  could  inspire  treatment  strategies  in which  targeted  inhibitors  of  evolvability  mechanisms  will  be  given  alongside  antibiotics  to slow down resistance evolution and extend theefficacy of antibiotics.We implemented  astochasticpopulation  genetics  model, toverifyways  in  which  general properties,  namely,  dose-response  characteristics  of  drugs  and  mutation  rates,  influence evolutionary  dynamics.  In  particular,  under  the  exposure  to  antibiotics  with  shallow  dose-response  curves,bacteria  have  narrower  distributions  of  fitness  effects  of  new  mutations. We  show  that in  silicothis  also  leads  to  slower  resistance  evolution.  We see and  confirm with experiments that increased mutation rates, apart from speeding up evolution, also leadto high reproducibility of phenotypic adaptation in a context of continually strong selection pressure.Knowledge  of  these  patterns  can  aid  in  predicting  the  dynamics  of  antibiotic resistance evolutionand adapting treatment schemes accordingly.Focusing on   a   previously   described   type   of   evolvability   modifier –a   stress-induced mutagenesis  allele –we  find  conditions  under  which  it  can  persist  in  a  population  under periodic  selectionakin  to  clinical  treatment. We  set  up  a  deterministic infinite  populationcontinuous  time  model  tracking  the  frequencies  of  a  mutator  and  resistance  allele  and evaluate  various  treatment  schemes  in  how  well  they  maintain  a stress-induced mutator allele. In particular,a high diversity  of stresses  is  crucial  for  the  persistence of the  mutator allele. This leads to a general trade-off where exactly those diversifying treatment schemes which  are  likely  to  decrease  levels  of  resistance  could  lead  to  stronger  selection  of  highly evolvable genotypes.In  the  long  run,  this  work  will  lead  to  a  deeper  understanding  of  the  genetic  and  cellular mechanisms involved in antibiotic resistance evolution and could inspire new strategies for slowing down its rate. "}],"doi":"10.15479/AT:ISTA:th1072","date_updated":"2026-07-30T14:47:59Z","oa":1,"date_published":"2018-12-28T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2019-04-09T13:57:15Z","department":[{"_id":"ToBo"},{"_id":"GradSch"}],"author":[{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"}],"file":[{"date_created":"2019-04-09T13:49:24Z","checksum":"fc60585c9eaad868ac007004ef130908","creator":"dernst","content_type":"application/pdf","file_size":5656866,"file_id":"6264","access_level":"open_access","date_updated":"2021-02-11T11:17:17Z","embargo":"2020-01-25","file_name":"2018_Thesis_Lukacisinova.pdf","relation":"main_file"},{"embargo_to":"open_access","relation":"source_file","file_name":"2018_Thesis_Lukacisinova_source.docx","access_level":"closed","file_id":"6265","date_updated":"2020-07-14T12:47:25Z","file_size":5168054,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-09T13:49:23Z","creator":"dernst","checksum":"264057ec0a92ab348cc83b41f021ba92"}],"page":"91","month":"12","supervisor":[{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2018"},{"related_material":{"record":[{"id":"449","status":"public","relation":"part_of_dissertation"}]},"citation":{"ama":"Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017.","apa":"Prat, T. (2017). <i>Identification of novel regulators of PIN polarity and development of novel auxin sensor</i>. Institute of Science and Technology Austria.","short":"T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.","mla":"Prat, Tomas. <i>Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor</i>. Institute of Science and Technology Austria, 2017.","chicago":"Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.","ieee":"T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017.","ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria."},"_id":"1127","oa_version":"Published Version","OA_place":"publisher","file_date_updated":"2021-02-22T11:52:56Z","title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","degree_awarded":"PhD","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"12","acknowledgement":"I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much.","publist_id":"6233","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","doi_confirm":"1","file":[{"date_updated":"2019-04-05T08:45:14Z","access_level":"closed","file_id":"6209","relation":"main_file","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","creator":"dernst","checksum":"d192c7c6c5ea32c8432437286dc4909e","date_created":"2019-04-05T08:45:14Z","content_type":"application/pdf","file_size":10285946},{"file_name":"2017_Thesis_Prat.pdf","relation":"main_file","date_updated":"2021-02-22T11:52:56Z","file_id":"9185","access_level":"open_access","content_type":"application/pdf","file_size":9802991,"success":1,"checksum":"bab18b52cf98145926042d8ed99fdb3b","creator":"dernst","date_created":"2021-02-22T11:52:56Z"}],"page":"131","department":[{"_id":"JiFr"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:17Z","author":[{"full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"month":"01","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2017","corr_author":"1","ddc":["580"],"type":"dissertation","abstract":[{"text":"Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes.","lang":"eng"}],"date_updated":"2026-07-29T12:01:27Z","oa":1,"date_published":"2017-01-12T00:00:00Z","article_processing_charge":"No"},{"related_material":{"record":[{"relation":"popular_science","id":"5568","status":"public"},{"id":"1362","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1633"}]},"citation":{"apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017."},"_id":"839","oa_version":"Published Version","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"OA_place":"publisher","file_date_updated":"2020-07-14T12:48:13Z","title":"Brittle fracture simulation with boundary elements for computer graphics","degree_awarded":"PhD","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"14","acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","publist_id":"6809","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","doi_confirm":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","file":[{"content_type":"application/pdf","file_size":14596191,"date_created":"2018-12-12T10:14:46Z","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","creator":"system","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","relation":"main_file","file_id":"5100","access_level":"open_access","date_updated":"2020-07-14T12:48:13Z"},{"checksum":"421672f68d563b029869c5cf1713f919","creator":"dernst","date_created":"2019-04-05T08:40:30Z","content_type":"application/zip","file_size":15060566,"date_updated":"2020-07-14T12:48:13Z","file_id":"6207","access_level":"closed","file_name":"2017_thesis_Hahn_source.zip","relation":"source_file"}],"page":"124","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:47Z","department":[{"_id":"ChWo"},{"_id":"GradSch"}],"author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Hahn","full_name":"Hahn, David"}],"supervisor":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"month":"08","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2017","pubrep_id":"855","corr_author":"1","ddc":["004","005","006","531","621"],"type":"dissertation","abstract":[{"text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ","lang":"eng"}],"ec_funded":1,"date_updated":"2026-07-29T13:27:25Z","oa":1,"doi":"10.15479/AT:ISTA:th_855","date_published":"2017-08-14T00:00:00Z","article_processing_charge":"No"},{"doi":"10.15479/at:ista:1130","oa":1,"date_updated":"2026-04-09T10:54:01Z","article_processing_charge":"No","date_published":"2016-07-07T00:00:00Z","type":"dissertation","ddc":["000"],"corr_author":"1","ec_funded":1,"abstract":[{"lang":"eng","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."}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"year":"2016","author":[{"orcid":"0000-0003-4409-8487","last_name":"Tarrach","full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten"}],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:19Z","language":[{"iso":"eng"}],"page":"151","file":[{"file_size":1523935,"success":1,"content_type":"application/pdf","date_created":"2021-02-22T11:39:32Z","checksum":"319a506831650327e85376db41fc1094","creator":"dernst","file_name":"2016_Tarrach_Thesis.pdf","relation":"main_file","file_id":"9179","access_level":"open_access","date_updated":"2021-02-22T11:39:32Z"},{"content_type":"application/pdf","file_size":1306068,"date_created":"2021-11-16T14:14:38Z","checksum":"39efcd789f0ad859ff15652cb7afc412","creator":"cchlebak","file_name":"2016_Tarrach_Thesispdfa.pdf","relation":"main_file","file_id":"10296","access_level":"closed","date_updated":"2021-11-17T13:46:55Z"}],"main_file_link":[{"open_access":"1","url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf"}],"supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"month":"07","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","publication_status":"published","publist_id":"6230","day":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Automatic synthesis of synchronisation primitives for concurrent programs","file_date_updated":"2021-11-17T13:46:55Z","OA_place":"publisher","degree_awarded":"PhD","citation":{"ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","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>.","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>.","short":"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>"},"related_material":{"record":[{"id":"2218","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2445"},{"relation":"part_of_dissertation","status":"public","id":"1729"}]},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"_id":"1130","oa_version":"Published Version"},{"project":[{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","_id":"1121","citation":{"apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016."},"degree_awarded":"PhD","title":"Selective barriers to horizontal gene transfer","file_date_updated":"2021-02-22T11:51:13Z","OA_place":"publisher","publist_id":"6239","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.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_status":"published","doi_confirm":"1","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","month":"12","supervisor":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"author":[{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","first_name":"Hande","orcid":"0000-0003-1986-9753","last_name":"Acar","full_name":"Acar, Hande"}],"department":[{"_id":"JoBo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:16Z","page":"75","file":[{"relation":"main_file","file_name":"PhDThesis_HandeAcar_1230.pdf","date_updated":"2019-08-13T11:17:50Z","access_level":"closed","file_id":"6814","content_type":"application/pdf","file_size":3682711,"creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4","date_created":"2019-08-13T11:17:50Z"},{"date_created":"2021-02-22T11:51:13Z","creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4","success":1,"file_size":3682711,"content_type":"application/pdf","access_level":"open_access","file_id":"9184","date_updated":"2021-02-22T11:51:13Z","relation":"main_file","file_name":"2016_Thesis_HandeAcar.pdf"}],"year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"abstract":[{"lang":"eng","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."}],"type":"dissertation","ddc":["570"],"corr_author":"1","article_processing_charge":"No","date_published":"2016-12-01T00:00:00Z","oa":1,"date_updated":"2026-07-29T11:17:47Z"},{"_id":"1122","oa_version":"Published Version","related_material":{"record":[{"relation":"other","status":"public","id":"5558"}]},"citation":{"short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","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>.","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>.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","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>","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>"},"degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2018-12-12T10:13:02Z","title":"Tracking, correcting and absorbing water surface waves","day":"15","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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. ","publist_id":"6238","publication_status":"published","doi_confirm":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","status":"public","has_accepted_license":"1","month":"07","supervisor":[{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":13869345,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:13:02Z","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","relation":"main_file","date_updated":"2018-12-12T10:13:02Z","file_id":"4982","access_level":"open_access"}],"page":"114","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:16Z","author":[{"first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","last_name":"Bojsen-Hansen"}],"year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"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."}],"corr_author":"1","ddc":["004","005","006","532","621"],"type":"dissertation","date_published":"2016-07-15T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:25:14Z","oa":1,"doi":"10.15479/AT:ISTA:th_640"},{"month":"02","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"_id":"1397","oa_version":"None","citation":{"ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","chicago":"Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016.","mla":"Chmelik, Martin. <i>Algorithms for Partially Observable Markov Decision Processes</i>. Institute of Science and Technology Austria, 2016.","short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","apa":"Chmelik, M. (2016). <i>Algorithms for partially observable markov decision processes</i>. Institute of Science and Technology Austria.","ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016."},"author":[{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:47Z","page":"232","degree_awarded":"PhD","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"title":"Algorithms for partially observable markov decision processes","OA_place":"publisher","publist_id":"5810","abstract":[{"text":"We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. Based on our theoretical algorithms we also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely. We show that for general integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where  given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","type":"dissertation","publication_status":"published","corr_author":"1","article_processing_charge":"No","doi_confirm":"1","date_published":"2016-02-01T00:00:00Z","status":"public","publisher":"Institute of Science and Technology Austria","date_updated":"2026-07-29T11:15:18Z"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"degree_awarded":"PhD","title":"Quantitative analysis of haptotactic cell migration","file_date_updated":"2021-02-22T11:43:14Z","OA_place":"publisher","oa_version":"Published Version","_id":"1129","citation":{"apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016."},"doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","publist_id":"6231","acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_status":"published","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"month":"07","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz","full_name":"Schwarz, Jan"}],"date_created":"2018-12-11T11:50:18Z","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"GradSch"}],"page":"178","file":[{"date_updated":"2019-08-13T10:55:35Z","file_id":"6813","access_level":"closed","file_name":"Thesis_JSchwarz_final.pdf","relation":"main_file","checksum":"e3cd6b28f9c5cccb8891855565a2dade","creator":"dernst","date_created":"2019-08-13T10:55:35Z","file_size":32044069,"content_type":"application/pdf"},{"date_updated":"2021-02-22T11:43:14Z","access_level":"open_access","file_id":"9181","relation":"main_file","file_name":"2016_Thesis_JSchwarz.pdf","creator":"dernst","checksum":"c3dbe219acf87eed2f46d21d5cca00de","date_created":"2021-02-22T11:43:14Z","file_size":8396717,"content_type":"application/pdf","success":1}],"article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","oa":1,"date_updated":"2026-07-29T11:30:22Z","abstract":[{"lang":"eng","text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale."}],"type":"dissertation","ddc":["570"],"corr_author":"1"},{"degree_awarded":"PhD","file_date_updated":"2021-02-22T11:36:34Z","OA_place":"publisher","title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","_id":"1123","oa_version":"Published Version","citation":{"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.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 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.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” 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.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","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."},"related_material":{"record":[{"id":"2159","status":"public","relation":"part_of_dissertation"}]},"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","status":"public","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.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publist_id":"6237","publication_status":"published","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"month":"08","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"page":"55","file":[{"date_updated":"2019-08-13T08:45:27Z","access_level":"closed","file_id":"6809","relation":"main_file","file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","creator":"dernst","checksum":"2d140cc924cd1b764544906fc22684ef","date_created":"2019-08-13T08:45:27Z","content_type":"application/pdf","file_size":2227916},{"file_name":"2016_Mabillard_Thesis.pdf","relation":"main_file","date_updated":"2021-02-22T11:36:34Z","file_id":"9178","access_level":"open_access","file_size":2227916,"success":1,"content_type":"application/pdf","checksum":"2d140cc924cd1b764544906fc22684ef","creator":"dernst","date_created":"2021-02-22T11:36:34Z"}],"author":[{"first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","last_name":"Mabillard"}],"department":[{"_id":"UlWa"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:16Z","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2016-08-01T00:00:00Z","oa":1,"date_updated":"2026-07-29T11:26:07Z","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.     "}],"ddc":["500"],"corr_author":"1","type":"dissertation"},{"article_processing_charge":"No","date_published":"2016-11-01T00:00:00Z","doi":"10.15479/AT:ISTA:TH_776","oa":1,"date_updated":"2026-07-29T11:28:23Z","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"type":"dissertation","ddc":["006"],"corr_author":"1","pubrep_id":"776","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"month":"11","supervisor":[{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia"}],"date_created":"2018-12-11T11:50:17Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"page":"127","file":[{"date_created":"2018-12-12T10:14:07Z","creator":"system","content_type":"application/pdf","file_size":2140062,"access_level":"open_access","file_id":"5056","date_updated":"2018-12-12T10:14:07Z","relation":"main_file","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf"}],"doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","publist_id":"6234","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.","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","degree_awarded":"PhD","title":"Theoretical foundations of multi-task lifelong learning","file_date_updated":"2018-12-12T10:14:07Z","OA_place":"publisher","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","_id":"1126","citation":{"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>.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","ieee":"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>.","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","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>","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>"}},{"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publist_id":"6235","publication_status":"published","degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2021-02-22T13:42:47Z","title":"Evolutionary proccesses in variable emvironments","_id":"1125","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2023"}]},"citation":{"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.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria."},"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:27:43Z","oa":1,"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"}],"corr_author":"1","ddc":["576"],"type":"dissertation","year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"month":"07","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"file":[{"relation":"main_file","file_name":"Novak_thesis.pdf","access_level":"closed","file_id":"6811","date_updated":"2019-08-13T09:01:00Z","file_size":3564901,"content_type":"application/pdf","date_created":"2019-08-13T09:01:00Z","creator":"dernst","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e"},{"creator":"dernst","checksum":"30808d2f7ca920e09f63a95cdc49bffd","date_created":"2021-02-22T13:42:47Z","file_size":2814384,"content_type":"application/pdf","success":1,"date_updated":"2021-02-22T13:42:47Z","access_level":"open_access","file_id":"9186","relation":"main_file","file_name":"2016_Novak_Thesis.pdf"}],"page":"124","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:17Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"author":[{"orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}]},{"supervisor":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"month":"08","file":[{"checksum":"ec453918c3bf8e6f460fd1156ef7b493","creator":"dernst","date_created":"2019-08-13T11:46:25Z","content_type":"application/pdf","file_size":2614660,"date_updated":"2019-08-13T11:46:25Z","file_id":"6815","access_level":"closed","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","relation":"main_file"},{"content_type":"application/pdf","success":1,"file_size":6096178,"date_created":"2020-09-21T11:30:40Z","creator":"dernst","checksum":"51ae398166370d18fd22478b6365c4da","relation":"main_file","file_name":"Thesis_Georg_Rieckh.pdf","access_level":"open_access","file_id":"8542","date_updated":"2020-09-21T11:30:40Z"}],"page":"114","date_created":"2018-12-11T11:50:18Z","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"}],"year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"abstract":[{"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.","lang":"eng"}],"corr_author":"1","ddc":["570"],"type":"dissertation","date_published":"2016-08-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:29:22Z","oa":1,"oa_version":"Published Version","_id":"1128","citation":{"ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","chicago":"Rieckh, Georg. “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.","short":"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.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016."},"degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2020-09-21T11:30:40Z","title":"Studying the complexities of transcriptional regulation","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"6232","publication_status":"published","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public"},{"_id":"1124","oa_version":"Published Version","citation":{"ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria.","short":"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.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria."},"degree_awarded":"PhD","title":"Optical functionalization of human class A orphan G-protein coupled receptors","OA_place":"publisher","file_date_updated":"2021-02-22T11:42:06Z","publist_id":"6236","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_status":"published","doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"month":"03","date_created":"2018-12-11T11:50:17Z","language":[{"iso":"eng"}],"department":[{"_id":"HaJa"},{"_id":"GradSch"}],"author":[{"last_name":"Morri","full_name":"Morri, Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio"}],"file":[{"content_type":"application/pdf","file_size":4785167,"checksum":"b439803ac0827cdddd56562a54e3b53b","creator":"dernst","date_created":"2019-08-13T10:50:00Z","file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","relation":"main_file","date_updated":"2019-08-13T10:50:00Z","file_id":"6812","access_level":"closed"},{"date_updated":"2021-02-22T11:42:06Z","file_id":"9180","access_level":"open_access","file_name":"2016_MORRI_Thesis.pdf","relation":"main_file","checksum":"dd4136247fe472e7d47880ec68ac8de0","creator":"dernst","date_created":"2021-02-22T11:42:06Z","file_size":4495669,"content_type":"application/pdf","success":1}],"page":"129","year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"type":"dissertation","corr_author":"1","ddc":["570"],"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:26:59Z","oa":1},{"title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","OA_place":"publisher","file_date_updated":"2021-02-22T11:48:44Z","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"1432","relation":"part_of_dissertation"}]},"citation":{"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.","chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016.","mla":"Mishra, Rajiv Kumar. <i>Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus</i>. Institute of Science and Technology Austria, 2016.","short":"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.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016."},"_id":"1396","oa_version":"Published Version","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","publication_status":"published","publist_id":"5811","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:46Z","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"author":[{"first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar","last_name":"Mishra"}],"file":[{"file_size":2407572,"content_type":"application/pdf","date_created":"2019-08-09T12:14:46Z","creator":"dernst","checksum":"5a010a838faf040f7064f3cfb802f743","relation":"main_file","file_name":"Thesis_Mishra_Rajiv (Final).pdf","access_level":"closed","file_id":"6782","date_updated":"2020-07-14T12:44:48Z"},{"file_size":2407572,"success":1,"content_type":"application/pdf","date_created":"2021-02-22T11:48:44Z","creator":"dernst","checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","relation":"main_file","file_name":"2016_RajivMishra_Thesis.pdf","access_level":"open_access","file_id":"9183","date_updated":"2021-02-22T11:48:44Z"}],"page":"83","month":"03","supervisor":[{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"date_updated":"2026-07-29T11:31:52Z","oa":1,"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","type":"dissertation","corr_author":"1","ddc":["570"],"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"}]},{"citation":{"ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016."},"related_material":{"record":[{"relation":"research_data","status":"public","id":"5554"},{"status":"public","id":"1666","relation":"part_of_dissertation"}]},"oa_version":"Published Version","_id":"1131","title":"Evolution of transcriptional regulatory sequences","file_date_updated":"2021-02-22T11:45:20Z","OA_place":"publisher","degree_awarded":"PhD","publication_status":"published","publist_id":"6229","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.","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","author":[{"full_name":"Tugrul, Murat","last_name":"Tugrul","orcid":"0000-0002-8523-0758","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:50:19Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"page":"89","file":[{"checksum":"66cb61a59943e4fb7447c6a86be5ef51","creator":"dernst","date_created":"2019-08-13T08:53:52Z","file_size":3695257,"content_type":"application/pdf","date_updated":"2019-08-13T08:53:52Z","file_id":"6810","access_level":"closed","file_name":"Tugrul_thesis_w_signature_page.pdf","relation":"main_file"},{"access_level":"open_access","file_id":"9182","date_updated":"2021-02-22T11:45:20Z","relation":"main_file","file_name":"2016_Tugrul_Thesis.pdf","date_created":"2021-02-22T11:45:20Z","creator":"dernst","checksum":"293e388d70563760f6b24c3e66283dda","content_type":"application/pdf","success":1,"file_size":3880811}],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"07","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"year":"2016","type":"dissertation","ddc":["576"],"corr_author":"1","abstract":[{"lang":"eng","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."}],"oa":1,"date_updated":"2026-07-29T11:31:14Z","article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z"},{"pubrep_id":"526","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"month":"02","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis","full_name":"Ellis, Thomas"}],"date_created":"2018-12-11T11:51:47Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"page":"130","file":[{"file_name":"2016_Thesis_Ellis_noSignatures.pdf","relation":"main_file","file_id":"19957","access_level":"open_access","date_updated":"2025-07-03T06:24:17Z","file_size":7590862,"content_type":"application/pdf","date_created":"2025-07-03T06:24:17Z","checksum":"f0f7c260e19ec1416824b165afe2d5fd","creator":"dernst"},{"file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","relation":"main_file","date_updated":"2025-07-03T06:24:39Z","file_id":"5106","access_level":"closed","file_size":11928241,"content_type":"application/pdf","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","creator":"system","date_created":"2018-12-12T10:14:51Z"}],"article_processing_charge":"No","date_published":"2016-02-18T00:00:00Z","doi":"10.15479/AT:ISTA:TH_526 ","oa":1,"date_updated":"2026-07-30T14:56:14Z","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"}],"type":"dissertation","ddc":["576"],"corr_author":"1","degree_awarded":"PhD","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","file_date_updated":"2025-07-03T06:24:39Z","OA_place":"publisher","oa_version":"Published Version","_id":"1398","citation":{"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>","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>","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.","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>.","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>.","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.","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."},"related_material":{"record":[{"id":"5553","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5551","status":"public"},{"relation":"part_of_dissertation","id":"5552","status":"public"}]},"doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","publist_id":"5809","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. ","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","publication_status":"published"},{"publisher":"Institute of Science and Technology Austria","status":"public","has_accepted_license":"1","publication_status":"published","day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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. ","publist_id":"5806","OA_place":"publisher","file_date_updated":"2021-11-17T13:47:24Z","title":"Learning with attributes for object recognition: Parametric and non-parametrics views","degree_awarded":"PhD","citation":{"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.","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>.","short":"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>","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>"},"_id":"1401","oa_version":"Published Version","date_updated":"2026-04-09T14:25:49Z","oa":1,"doi":"10.15479/at:ista:1401","date_published":"2015-04-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","ddc":["000"],"type":"dissertation","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."}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2015","file":[{"content_type":"application/pdf","success":1,"file_size":7964342,"creator":"dernst","checksum":"3605b402bb6934e09ae4cf672c84baf7","date_created":"2021-02-22T11:33:17Z","relation":"main_file","file_name":"2015_Thesis_Sharmanska.pdf","date_updated":"2021-02-22T11:33:17Z","access_level":"open_access","file_id":"9177"},{"date_updated":"2021-11-17T13:47:24Z","file_id":"10297","access_level":"closed","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","relation":"main_file","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","creator":"cchlebak","date_created":"2021-11-16T14:40:45Z","file_size":7372241,"content_type":"application/pdf"}],"page":"144","date_created":"2018-12-11T11:51:48Z","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"},{"_id":"GradSch"}],"author":[{"last_name":"Sharmanska","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia"}],"month":"04","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}]},{"type":"dissertation","publication_status":"published","corr_author":"1","abstract":[{"lang":"eng","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."}],"publist_id":"5808","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","status":"public","publisher":"Institute of Science and Technology Austria","date_updated":"2026-07-29T10:08:34Z","article_processing_charge":"No","date_published":"2015-06-01T00:00:00Z","doi_confirm":"1","citation":{"apa":"Pausinger, F. (2015). <i>On the approximation of intrinsic volumes</i>. Institute of Science and Technology Austria.","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.","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.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","mla":"Pausinger, Florian. <i>On the Approximation of Intrinsic Volumes</i>. Institute of Science and Technology Austria, 2015."},"author":[{"first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","last_name":"Pausinger"}],"related_material":{"record":[{"status":"public","id":"1662","relation":"part_of_dissertation"},{"status":"public","id":"1792","relation":"part_of_dissertation"},{"status":"public","id":"2255","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:48Z","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"page":"144","month":"06","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"_id":"1399","oa_version":"None","alternative_title":["ISTA Thesis"],"title":"On the approximation of intrinsic volumes","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","degree_awarded":"PhD","year":"2015"},{"_id":"1400","oa_version":"None","month":"04","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"page":"183","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2000"},{"relation":"part_of_dissertation","status":"public","id":"1709"},{"id":"2858","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"2816","relation":"part_of_dissertation"},{"status":"public","id":"2247","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"3260","status":"public"},{"id":"3157","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:48Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"citation":{"ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","mla":"Reiter, Johannes. <i>The Subclonal Evolution of Cancer</i>. Institute of Science and Technology Austria, 2015.","short":"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."},"author":[{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"}],"year":"2015","degree_awarded":"PhD","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"title":"The subclonal evolution of cancer","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","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","corr_author":"1","publication_status":"published","type":"dissertation","doi_confirm":"1","date_published":"2015-04-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T10:15:25Z","publisher":"Institute of Science and Technology Austria","status":"public"}]