[{"year":"2018","page":"95","abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. ","lang":"eng"}],"oa_version":"Published Version","date_created":"2019-04-09T14:13:39Z","related_material":{"record":[{"status":"public","id":"7132","relation":"new_edition"}]},"status":"public","file":[{"file_id":"6267","creator":"dernst","file_name":"2018_Thesis_McKenzie.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2019-11-24","file_size":4906420,"checksum":"9d2c2dca04b00e485470c28b262af59a","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-09T14:12:40Z"},{"creator":"dernst","file_id":"6268","file_name":"2018_Thesis_McKenzie_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_size":5053545,"checksum":"50b58c272899601bc6fd9642c4dc97f1","date_updated":"2020-07-14T12:47:25Z","embargo_to":"open_access","date_created":"2019-04-09T14:12:40Z"}],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","language":[{"iso":"eng"}],"_id":"6266","month":"10","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine"}],"publication_status":"published","date_updated":"2026-04-08T14:14:05Z","ddc":["571","573"],"doi":"10.15479/at:ista:th_1055","oa":1,"type":"dissertation","file_date_updated":"2021-02-11T11:17:16Z","corr_author":"1","has_accepted_license":"1","pubrep_id":"1055","supervisor":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>.","apa":"Mckenzie, C. (2018). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>"},"department":[{"_id":"HaJa"}],"OA_place":"publisher","date_published":"2018-10-31T00:00:00Z","day":"31"},{"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018.","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"CaGu"}],"pubrep_id":"1059","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"30","OA_place":"publisher","date_published":"2018-10-30T00:00:00Z","type":"dissertation","file_date_updated":"2021-02-11T11:17:14Z","doi":"10.15479/AT:ISTA:th1059","oa":1,"has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"_id":"26","status":"public","file":[{"file_size":9190845,"checksum":"413cbce1cd1debeae3abe2a25dbc70d1","date_updated":"2020-07-14T12:45:43Z","date_created":"2019-02-08T10:51:22Z","embargo_to":"open_access","creator":"dernst","file_id":"5941","file_name":"Thesis_Steinrueck_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"embargo":"2019-11-02","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Thesis_Steinrueck_final.pdf","creator":"dernst","file_id":"5942","date_created":"2019-02-08T10:51:22Z","date_updated":"2021-02-11T11:17:14Z","checksum":"3def8b7854c8b42d643597ce0215efac","file_size":7521973}],"title":"The influence of sequence context on the evolution of bacterial gene expression","publication_status":"published","date_updated":"2026-04-08T14:15:35Z","ddc":["576","579"],"author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","full_name":"Steinrück, Magdalena","first_name":"Magdalena","orcid":"0000-0003-1229-9719"}],"month":"10","page":"109","publist_id":"8029","abstract":[{"lang":"eng","text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer."}],"year":"2018","related_material":{"record":[{"relation":"part_of_dissertation","id":"704","status":"public"}]},"date_created":"2018-12-11T11:44:14Z","oa_version":"Published Version"},{"has_accepted_license":"1","corr_author":"1","type":"dissertation","file_date_updated":"2021-02-11T23:30:21Z","doi":"10.15479/AT:ISTA:TH_1031","oa":1,"day":"22","OA_place":"publisher","date_published":"2018-06-22T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Capek D. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>","short":"D. Capek, Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration, Institute of Science and Technology Austria, 2018.","mla":"Capek, Daniel. <i>Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">10.15479/AT:ISTA:TH_1031</a>.","ista":"Capek D. 2018. Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration. Institute of Science and Technology Austria.","chicago":"Capek, Daniel. “Optogenetic Frizzled 7 Reveals a Permissive Function of Wnt/PCP Signaling in Directed Mesenchymal Cell Migration.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>.","ieee":"D. Capek, “Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration,” Institute of Science and Technology Austria, 2018.","apa":"Capek, D. (2018). <i>Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1031\">https://doi.org/10.15479/AT:ISTA:TH_1031</a>"},"pubrep_id":"1031","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"661","relation":"part_of_dissertation","status":"public"},{"id":"1100","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"676","status":"public"}]},"date_created":"2018-12-11T11:44:21Z","oa_version":"Published Version","page":"95","publist_id":"8004","abstract":[{"lang":"eng","text":"The Wnt/planar cell polarity (Wnt/PCP) pathway determines planar polarity of epithelial cells in both vertebrates and invertebrates. The role that Wnt/PCP signaling plays in mesenchymal contexts, however, is only poorly understood. While previous studies have demonstrated the capacity of Wnt/PCP signaling to polarize and guide directed migration of mesenchymal cells, it remains unclear whether endogenous Wnt/PCP signaling performs these functions instructively, as it does in epithelial cells. Here we developed a light-switchable version of the Wnt/PCP receptor Frizzled 7 (Fz7) to unambiguously distinguish between an instructive and a permissive role of Wnt/PCP signaling for the directional collective migration of mesendoderm progenitor cells during zebrafish gastrulation. We show that prechordal plate (ppl) cell migration is defective in maternal-zygotic fz7a and fz7b (MZ fz7a,b) double mutant embryos, and that Fz7 functions cell-autonomously in this process by promoting ppl cell protrusion formation and directed migration. We further show that local activation of Fz7 can direct ppl cell migration both in vitro and in vivo. Surprisingly, however, uniform Fz7 activation is sufficient to fully rescue the ppl cell migration defect in MZ fz7a,b mutant embryos, indicating that Wnt/PCP signaling functions permissively rather than instructively in directed mesendoderm cell migration during zebrafish gastrulation."}],"year":"2018","publication_status":"published","date_updated":"2026-04-16T10:07:33Z","ddc":["570","591","596"],"author":[{"last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","full_name":"Capek, Daniel"}],"month":"06","language":[{"iso":"eng"}],"_id":"50","file":[{"date_updated":"2021-02-11T11:17:17Z","date_created":"2019-04-08T13:42:26Z","file_size":31576521,"checksum":"d3eca3dcacb67bffdde6e6609c31cdd0","file_name":"2018_Thesis_Capek.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2019-06-25","file_id":"6238","creator":"dernst"},{"date_updated":"2021-02-11T23:30:21Z","embargo_to":"open_access","date_created":"2019-04-08T13:42:27Z","file_size":38992956,"checksum":"876deb14067e638aba65d209668bd821","file_name":"2018_Thesis_Capek_source.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"dernst","file_id":"6239"}],"status":"public","title":"Optogenetic Frizzled 7 reveals a permissive function of Wnt/PCP signaling in directed mesenchymal cell migration"},{"page":"87","publist_id":"6829","ec_funded":1,"abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"year":"2017","project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"date_created":"2018-12-11T11:48:41Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"820","status":"public","file":[{"date_created":"2018-12-12T10:17:00Z","date_updated":"2020-07-14T12:48:10Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","file_size":3417773,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","creator":"system","file_id":"5252"},{"file_name":"2017_thesis_Jesse_source.tex","content_type":"application/x-tex","access_level":"closed","relation":"source_file","creator":"dernst","file_id":"6212","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T08:51:59Z","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_size":215899}],"title":"The lac operon in the wild","publication_status":"published","date_updated":"2026-04-08T14:18:16Z","ddc":["576","577","579"],"author":[{"last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne","first_name":"Fabienne"}],"month":"08","type":"dissertation","file_date_updated":"2020-07-14T12:48:10Z","doi":"10.15479/AT:ISTA:th_857","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"JoBo"}],"citation":{"ama":"Jesse F. The lac operon in the wild. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","mla":"Jesse, Fabienne. <i>The Lac Operon in the Wild</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","apa":"Jesse, F. (2017). <i>The lac operon in the wild</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>."},"article_processing_charge":"No","pubrep_id":"857","supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"publication_identifier":{"issn":["2663-337X"]},"day":"25","OA_place":"publisher","date_published":"2017-08-25T00:00:00Z"},{"abstract":[{"lang":"eng","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."}],"page":"131","publist_id":"6233","year":"2017","date_created":"2018-12-11T11:50:17Z","related_material":{"record":[{"status":"public","id":"449","relation":"part_of_dissertation"}]},"oa_version":"Published Version","_id":"1127","language":[{"iso":"eng"}],"status":"public","file":[{"file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","access_level":"closed","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"6209","date_updated":"2019-04-05T08:45:14Z","date_created":"2019-04-05T08:45:14Z","file_size":10285946,"checksum":"d192c7c6c5ea32c8432437286dc4909e"},{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2017_Thesis_Prat.pdf","creator":"dernst","file_id":"9185","date_created":"2021-02-22T11:52:56Z","success":1,"date_updated":"2021-02-22T11:52:56Z","file_size":9802991,"checksum":"bab18b52cf98145926042d8ed99fdb3b"}],"title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","ddc":["580"],"publication_status":"published","date_updated":"2026-04-08T14:17:39Z","author":[{"last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Prat, Tomas"}],"month":"01","type":"dissertation","file_date_updated":"2021-02-22T11:52:56Z","oa":1,"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.","has_accepted_license":"1","corr_author":"1","publisher":"Institute of Science and Technology Austria","citation":{"short":"T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017.","ama":"Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017.","ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ieee":"T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 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.","chicago":"Prat, Tomas. “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."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"JiFr"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"day":"12","date_published":"2017-01-12T00:00:00Z","OA_place":"publisher"},{"date_created":"2018-12-11T11:49:35Z","oa_version":"Published Version","publist_id":"6407","page":"97","ec_funded":1,"abstract":[{"text":"An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language).","lang":"eng"}],"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"year":"2017","date_updated":"2026-04-08T14:17:06Z","publication_status":"published","ddc":["004"],"author":[{"full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek"}],"month":"05","language":[{"iso":"eng"}],"_id":"992","title":"Complexity of constraint satisfaction","status":"public","file":[{"date_created":"2018-12-12T10:07:55Z","date_updated":"2020-07-14T12:48:18Z","checksum":"81761fb939acb7585c36629f765b4373","file_size":786145,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","file_id":"4654","creator":"system"},{"checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","file_size":5936337,"date_created":"2019-04-05T08:43:24Z","date_updated":"2020-07-14T12:48:18Z","creator":"dernst","file_id":"6208","content_type":"application/zip","access_level":"closed","relation":"source_file","file_name":"2017_Thesis_Rolinek_source.zip"}],"has_accepted_license":"1","acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","corr_author":"1","file_date_updated":"2020-07-14T12:48:18Z","type":"dissertation","doi":"10.15479/AT:ISTA:th_815","oa":1,"day":"01","OA_place":"publisher","date_published":"2017-05-01T00:00:00Z","degree_awarded":"PhD","citation":{"short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_815\">10.15479/AT:ISTA:th_815</a>","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","apa":"Rolinek, M. (2017). <i>Complexity of constraint satisfaction</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_815\">https://doi.org/10.15479/AT:ISTA:th_815</a>","chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_815\">https://doi.org/10.15479/AT:ISTA:th_815</a>.","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017.","mla":"Rolinek, Michal. <i>Complexity of Constraint Satisfaction</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_815\">10.15479/AT:ISTA:th_815</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"VlKo"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","pubrep_id":"815","supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]}},{"oa_version":"Published Version","date_created":"2019-04-09T15:16:45Z","year":"2017","page":"83","abstract":[{"text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.","lang":"eng"}],"author":[{"orcid":"0000-0002-2711-9453","first_name":"Pavel","full_name":"Payne, Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87"}],"month":"02","date_updated":"2026-04-08T14:16:28Z","publication_status":"published","ddc":["570"],"title":"Bacterial herd and social immunity to phages","status":"public","file":[{"file_name":"thesis_pavel_payne_final_w_signature_page.pdf","relation":"main_file","access_level":"closed","content_type":"application/pdf","file_id":"6292","creator":"dernst","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-09T15:15:32Z","file_size":3025175,"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f"},{"creator":"dernst","file_id":"9187","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2017_Payne_Thesis.pdf","file_size":3111536,"checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"date_created":"2021-02-22T13:45:59Z","date_updated":"2021-02-22T13:45:59Z"}],"language":[{"iso":"eng"}],"_id":"6291","corr_author":"1","has_accepted_license":"1","oa":1,"file_date_updated":"2021-02-22T13:45:59Z","type":"dissertation","OA_place":"publisher","date_published":"2017-02-01T00:00:00Z","day":"01","article_processing_charge":"No","supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","citation":{"short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). <i>Bacterial herd and social immunity to phages</i>. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","mla":"Payne, Pavel. <i>Bacterial Herd and Social Immunity to Phages</i>. Institute of Science and Technology Austria, 2017."},"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria"},{"related_material":{"record":[{"id":"5828","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-11T11:48:46Z","oa_version":"Published Version","publist_id":"6811","page":"93","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"year":"2017","date_updated":"2026-04-08T14:18:55Z","publication_status":"published","ddc":["571"],"month":"08","author":[{"first_name":"Haibing","full_name":"Xu, Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"_id":"837","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"2017_Xu_Haibing_Thesis_Source.docx","creator":"dernst","file_id":"6213","date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","file_size":3589490,"checksum":"f11925fbbce31e495124b6bc4f10573c"},{"checksum":"ffb10749a537d615fab1ef0937ccb157","file_size":11668613,"date_created":"2019-04-05T08:59:51Z","date_updated":"2020-07-14T12:48:12Z","file_id":"6214","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_Xu_Thesis_IST.pdf"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","corr_author":"1","file_date_updated":"2020-07-14T12:48:12Z","type":"dissertation","doi":"10.15479/AT:ISTA:th_858","oa":1,"day":"23","OA_place":"publisher","date_published":"2017-08-23T00:00:00Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"department":[{"_id":"JoCs"}],"citation":{"ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"pubrep_id":"858","publication_identifier":{"issn":["2663-337X"]}},{"article_processing_charge":"No","pubrep_id":"828","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"KrPi"}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria."},"OA_place":"publisher","date_published":"2017-06-26T00:00:00Z","day":"26","doi":"10.15479/AT:ISTA:th_828","oa":1,"type":"dissertation","file_date_updated":"2020-07-14T12:48:12Z","corr_author":"1","has_accepted_license":"1","status":"public","file":[{"file_size":847400,"checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_created":"2018-12-12T10:10:13Z","date_updated":"2020-07-14T12:48:12Z","file_id":"4799","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf"},{"checksum":"3462101745ce8ad199c2d0f75dae4a7e","file_size":26054879,"date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:24:11Z","creator":"dernst","file_id":"6202","file_name":"2017_Thesis_Rybar_source.zip","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"title":"(The exact security of) Message authentication codes","language":[{"iso":"eng"}],"_id":"838","author":[{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","full_name":"Rybar, Michal","first_name":"Michal"}],"month":"06","publication_status":"published","date_updated":"2026-04-08T14:18:39Z","ddc":["000"],"year":"2017","page":"86","publist_id":"6810","abstract":[{"text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ","lang":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:48:46Z","related_material":{"record":[{"status":"public","id":"2082","relation":"part_of_dissertation"},{"status":"public","id":"6196","relation":"part_of_dissertation"}]}},{"page":"86","abstract":[{"lang":"eng","text":"The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's."}],"year":"2017","date_created":"2019-04-09T15:04:32Z","related_material":{"record":[{"id":"87","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"5678","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"718","status":"public"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"6287","file":[{"file_id":"6289","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_Thesis_Nikitenko.pdf","checksum":"ece7e598a2f060b263c2febf7f3fe7f9","file_size":2324870,"date_created":"2019-04-09T14:54:51Z","date_updated":"2020-07-14T12:47:26Z"},{"date_updated":"2020-07-14T12:47:26Z","date_created":"2019-04-09T14:54:51Z","file_size":2863219,"checksum":"99b7ad76e317efd447af60f91e29b49b","file_name":"2017_Thesis_Nikitenko_source.zip","relation":"source_file","content_type":"application/zip","access_level":"closed","file_id":"6290","creator":"dernst"}],"status":"public","title":"Discrete Morse theory for random complexes ","publication_status":"published","date_updated":"2026-04-08T14:19:31Z","ddc":["514","516","519"],"author":[{"first_name":"Anton","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko"}],"month":"10","type":"dissertation","file_date_updated":"2020-07-14T12:47:26Z","doi":"10.15479/AT:ISTA:th_873","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_873\">10.15479/AT:ISTA:th_873</a>","short":"A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017.","mla":"Nikitenko, Anton. <i>Discrete Morse Theory for Random Complexes </i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_873\">10.15479/AT:ISTA:th_873</a>.","apa":"Nikitenko, A. (2017). <i>Discrete Morse theory for random complexes </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_873\">https://doi.org/10.15479/AT:ISTA:th_873</a>","ieee":"A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017.","chicago":"Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_873\">https://doi.org/10.15479/AT:ISTA:th_873</a>.","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"HeEd"}],"article_processing_charge":"No","pubrep_id":"873","supervisor":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"publication_identifier":{"issn":["2663-337X"]},"day":"27","OA_place":"publisher","date_published":"2017-10-27T00:00:00Z"},{"status":"public","file":[{"file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5100","creator":"system","date_updated":"2020-07-14T12:48:13Z","date_created":"2018-12-12T10:14:46Z","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","file_size":14596191},{"file_size":15060566,"checksum":"421672f68d563b029869c5cf1713f919","date_updated":"2020-07-14T12:48:13Z","date_created":"2019-04-05T08:40:30Z","creator":"dernst","file_id":"6207","file_name":"2017_thesis_Hahn_source.zip","access_level":"closed","content_type":"application/zip","relation":"source_file"}],"title":"Brittle fracture simulation with boundary elements for computer graphics","language":[{"iso":"eng"}],"_id":"839","author":[{"full_name":"Hahn, David","first_name":"David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"}],"month":"08","publication_status":"published","date_updated":"2026-04-08T14:20:16Z","ddc":["004","005","006","531","621"],"year":"2017","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"}],"page":"124","publist_id":"6809","ec_funded":1,"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","date_created":"2018-12-11T11:48:47Z","related_material":{"record":[{"id":"5568","relation":"popular_science","status":"public"},{"relation":"part_of_dissertation","id":"1362","status":"public"},{"relation":"part_of_dissertation","id":"1633","status":"public"}]},"supervisor":[{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"article_processing_charge":"No","pubrep_id":"855","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","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>.","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>","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.","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>"},"department":[{"_id":"ChWo"}],"OA_place":"publisher","date_published":"2017-08-14T00:00:00Z","day":"14","doi":"10.15479/AT:ISTA:th_855","oa":1,"type":"dissertation","file_date_updated":"2020-07-14T12:48:13Z","corr_author":"1","license":"https://creativecommons.org/licenses/by-sa/4.0/","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"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","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"_id":"202","status":"public","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","file_id":"4710","creator":"system","date_created":"2018-12-12T10:08:48Z","date_updated":"2020-07-14T12:45:24Z","file_size":18569590,"checksum":"33cfb59674e91f82e3738396d3fb3776"},{"date_updated":"2020-07-14T12:45:24Z","date_created":"2019-04-05T08:33:14Z","file_size":2801649,"checksum":"dcc239968decb233e7f98cf1083d8c26","file_name":"2017_Pleska_Maros_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"dernst","file_id":"6204"}],"title":"Biology of restriction-modification systems at the single-cell and population level","publication_status":"published","date_updated":"2026-04-08T14:19:44Z","ddc":["576","579"],"month":"10","author":[{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","first_name":"Maros"}],"page":"126","publist_id":"7711","abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"year":"2017","project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"}],"date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"457"},{"id":"561","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1243","relation":"part_of_dissertation"}]},"oa_version":"Published Version","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"CaGu"}],"article_processing_charge":"No","pubrep_id":"916","supervisor":[{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"}],"publication_identifier":{"issn":["2663-337X"]},"day":"01","OA_place":"publisher","date_published":"2017-10-01T00:00:00Z","type":"dissertation","file_date_updated":"2020-07-14T12:45:24Z","doi":"10.15479/AT:ISTA:th_916","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","has_accepted_license":"1","corr_author":"1"},{"year":"2017","page":"117","publist_id":"6483","abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:49:18Z","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"status":"public","file":[{"date_created":"2019-04-05T09:03:20Z","date_updated":"2020-07-14T12:48:15Z","checksum":"193425764d9aaaed3ac57062a867b315","file_size":46903863,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"2017_Adamowski-Thesis_Source.docx","creator":"dernst","file_id":"6215"},{"date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z","file_size":8698888,"checksum":"df5ab01be81f821e1b958596a1ec8d21","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2017_Adamowski-Thesis.pdf","creator":"dernst","file_id":"6216"}],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","language":[{"iso":"eng"}],"_id":"938","author":[{"orcid":"0000-0001-6463-5257","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"}],"month":"06","publication_status":"published","date_updated":"2026-04-08T14:20:45Z","ddc":["581","583","580"],"doi":"10.15479/AT:ISTA:th_842","oa":1,"type":"dissertation","file_date_updated":"2020-07-14T12:48:15Z","corr_author":"1","has_accepted_license":"1","pubrep_id":"842","supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"citation":{"mla":"Adamowski, Maciek. <i>Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana </i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). <i>Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"OA_place":"publisher","date_published":"2017-06-02T00:00:00Z","day":"02"},{"author":[{"full_name":"Mitosch, Karin","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch"}],"month":"09","publication_status":"published","date_updated":"2026-04-08T14:21:57Z","ddc":["571","579"],"status":"public","file":[{"date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","file_size":6331071,"checksum":"da3993c5f90f59a8e8623cc31ad501dd","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_KarinMitosch.docx","creator":"dernst","file_id":"6210"},{"checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_size":9289852,"date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T08:48:51Z","creator":"dernst","file_id":"6211","file_name":"Thesis_KarinMitosch.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","language":[{"iso":"eng"}],"_id":"818","oa_version":"Published Version","date_created":"2018-12-11T11:48:40Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"666"},{"status":"public","relation":"part_of_dissertation","id":"2001"}]},"year":"2017","page":"113","publist_id":"6831","abstract":[{"lang":"eng","text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. "}],"OA_place":"publisher","date_published":"2017-09-27T00:00:00Z","day":"27","supervisor":[{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"article_processing_charge":"No","pubrep_id":"862","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"ToBo"}],"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_862","oa":1,"type":"dissertation","file_date_updated":"2020-07-14T12:48:09Z"},{"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","apa":"Pavlogiannis, A. (2017). <i>Algorithmic advances in program analysis and their applications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>"},"department":[{"_id":"KrCh"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"854","article_processing_charge":"No","supervisor":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"day":"09","date_published":"2017-08-09T00:00:00Z","OA_place":"publisher","type":"dissertation","file_date_updated":"2020-07-14T12:48:10Z","oa":1,"doi":"10.15479/AT:ISTA:th_854","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","has_accepted_license":"1","tmp":{"short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png"},"license":"https://creativecommons.org/licenses/by-nd/4.0/","corr_author":"1","_id":"821","language":[{"iso":"eng"}],"file":[{"file_id":"4900","creator":"system","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_size":4103115,"date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-12T10:11:44Z"},{"file_name":"2017_thesis_Pavlogiannis.zip","relation":"source_file","content_type":"application/zip","access_level":"closed","file_id":"6201","creator":"dernst","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z","file_size":14744374,"checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83"}],"status":"public","title":"Algorithmic advances in program analysis and their applications","ddc":["000"],"publication_status":"published","date_updated":"2026-04-08T14:22:17Z","month":"08","author":[{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas"}],"abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"ec_funded":1,"page":"418","publist_id":"6828","year":"2017","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"date_created":"2018-12-11T11:48:41Z","related_material":{"record":[{"id":"1602","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1604","status":"public"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1071","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1607"},{"relation":"part_of_dissertation","id":"1714","status":"public"}]},"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"_id":"1155","status":"public","file":[{"checksum":"1406a681cb737508234fde34766be2c2","file_size":1028586,"date_updated":"2020-07-14T12:44:34Z","date_created":"2018-12-12T10:11:26Z","file_id":"4880","creator":"system","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"title":"Statistical and logical methods for property checking","publication_status":"published","date_updated":"2026-04-15T10:02:13Z","ddc":["004","005"],"month":"01","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw"}],"page":"163","publist_id":"6203","abstract":[{"lang":"eng","text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results."}],"ec_funded":1,"year":"2017","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"date_created":"2018-12-11T11:50:27Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2063"},{"id":"1093","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1391","status":"public"},{"id":"1234","relation":"part_of_dissertation","status":"public"},{"id":"1230","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"1501","status":"public"},{"status":"public","id":"1502","relation":"part_of_dissertation"},{"id":"2167","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">10.15479/AT:ISTA:TH_730</a>","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","mla":"Daca, Przemyslaw. <i>Statistical and Logical Methods for Property Checking</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">10.15479/AT:ISTA:TH_730</a>.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">https://doi.org/10.15479/AT:ISTA:TH_730</a>.","apa":"Daca, P. (2017). <i>Statistical and logical methods for property checking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">https://doi.org/10.15479/AT:ISTA:TH_730</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"730","publication_identifier":{"issn":["2663-337X"]},"day":"02","OA_place":"publisher","date_published":"2017-01-02T00:00:00Z","type":"dissertation","file_date_updated":"2020-07-14T12:44:34Z","doi":"10.15479/AT:ISTA:TH_730","oa":1,"acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","has_accepted_license":"1","corr_author":"1"},{"OA_place":"publisher","date_published":"2017-09-26T00:00:00Z","day":"26","supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","first_name":"Sylvia M"}],"article_processing_charge":"No","pubrep_id":"861","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"SyCr"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","ama":"Pull C. Disease defence in garden ants. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>.","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","apa":"Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>","mla":"Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>."},"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_861","oa":1,"type":"dissertation","file_date_updated":"2020-07-14T12:48:09Z","author":[{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"}],"month":"09","publication_status":"published","date_updated":"2026-04-16T10:07:02Z","ddc":["576","577","578","579","590","592"],"status":"public","file":[{"checksum":"4993cdd5382295758ecc3ecbd2a9aaff","file_size":18580400,"date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T07:53:04Z","creator":"dernst","file_id":"6199","file_name":"2017_Thesis_Pull.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"date_created":"2019-04-05T07:53:04Z","date_updated":"2020-07-14T12:48:09Z","checksum":"ee2e3ebb5b53c154c866f5b052b25153","file_size":14400681,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2017_Thesis_Pull.pdf","creator":"dernst","file_id":"6200"}],"title":"Disease defence in garden ants","language":[{"iso":"eng"}],"_id":"819","oa_version":"Published Version","date_created":"2018-12-11T11:48:40Z","related_material":{"record":[{"id":"806","relation":"part_of_dissertation","status":"public"},{"id":"616","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"732"},{"status":"public","id":"734","relation":"part_of_dissertation"}]},"year":"2017","page":"122","publist_id":"6830","abstract":[{"lang":"eng","text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. "}]},{"ddc":["570","590"],"publication_status":"published","date_updated":"2026-04-16T10:07:32Z","author":[{"last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","first_name":"Vanessa"}],"month":"03","_id":"961","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_id":"6205","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"2017_Barone_thesis_final.docx","file_size":14497822,"checksum":"242f88c87f2cf267bf05049fa26a687b","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z"},{"file_name":"2017_Barone_thesis_.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6206","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","file_size":14995941,"checksum":"ba5b0613ed8bade73a409acdd880fb8a"}],"status":"public","title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","date_created":"2018-12-11T11:49:25Z","related_material":{"record":[{"status":"public","id":"735","relation":"part_of_dissertation"},{"id":"1100","relation":"part_of_dissertation","status":"public"},{"id":"1537","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1912","relation":"part_of_dissertation"},{"id":"3246","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"2926","relation":"part_of_dissertation"},{"status":"public","id":"676","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cell-cell  contact  formation  constitutes  the  first  step  in  the  emergence  of  multicellularity  in evolution, thereby  allowing  the  differentiation  of  specialized  cell  types.  In  metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell   fate   specification   has   been   implicated   in   cell-cell  contact formation.   However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive  feedback  loop  between  cell-cell  contact  duration,  morphogen  signaling  and mesendoderm  cell  fate  specification  during  zebrafish  gastrulation.  We  show  that  long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to  respond  to  Nodal  signaling,  required  for  proper  ppl  cell  fate  specification.  We  further show  that  Nodal  signalling  romotes  ppl  cell-cell  contact  duration,  thereby  generating  an effective  positive  feedback  loop  between  ppl  cell-cell  contact  duration  and  cell  fate specification. Finally, by using a combination of theoretical modeling and experimentation, we  show  that  this  feedback  loop  determines  whether  anterior  axial  mesendoderm  cells become  ppl  progenitors  or,  instead,  turn  into  endoderm  progenitors.  Our  findings  reveal that  the  gene  regulatory  networks  leading  to  cell  fate  diversification  within  the  developing embryo  are  controlled  by  the  interdependent  activities  of  cell-cell  signaling  and  contact formation."}],"page":"109","publist_id":"6444","year":"2017","day":"01","date_published":"2017-03-01T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","mla":"Barone, Vanessa. <i>Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>.","apa":"Barone, V. (2017). <i>Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>"},"department":[{"_id":"CaHe"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"pubrep_id":"825","supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall  the  good  science  I  witnessed  and  participated  in.  It  has  been  a \r\nblast,  an  incredibly \r\nexciting  one!  Thanks  to  JLo,  for  teaching  me  how  to  master  my  pipettes  and  showing  me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout  zebrafish  and  being  always  there  to  advice,  sugge\r\nst,  support...and  play  fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether  for  all  the  good  laughs  we\r\nhad.  My  start  in  Vienna  would  have  been  a  lot  more \r\ndifficult  without  you  guys.  Also  it  would  not  have  been  possible  without  Elena  and  Inês: \r\nthanks  for  helping  setting  up  this  lab  and  for  the  dinners  in  Gugging.  Thanks  to  Martin,  for \r\nhelping  me  understand \r\nthe  physics  behind  biology.  Thanks  to  Philipp,  for  the  interest  and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.  To  Shayan,  for  being  such  a  motivated  student.  To  Matt,  for  helping  out\r\nwith  coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza,  for  the  wonderful  atmosphere  in  the  lab.  Many  than\r\nks  to  Koni  and  Deborah:  doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor  setting  up  an  amazing  imaging  facility  and  for  building  the  best  team,  Robert,  Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand  to  Patrick  Lemaire  f\r\nor  the  helpful  insight  and  extremely  interesting  discussion  we  had \r\nabout  the  project.  Also,  this  journey  would  not  have  been  the  same  without  all  the  friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie  ai  miei  fratelli,  Nunzio  e  William,  e  alla  mia  mamma,  per  essermi  sempre  vicini  pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","type":"dissertation","file_date_updated":"2020-07-14T12:48:16Z","oa":1,"doi":"10.15479/AT:ISTA:th_825"},{"oa_version":"None","corr_author":"1","date_created":"2018-12-11T11:51:47Z","year":"2016","type":"dissertation","page":"232","publist_id":"5810","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin"}],"month":"02","OA_place":"publisher","date_published":"2016-02-01T00:00:00Z","publication_status":"published","date_updated":"2026-04-08T14:23:19Z","day":"01","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"status":"public","title":"Algorithms for partially observable markov decision processes","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","_id":"1397","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"KrCh"}],"citation":{"short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016.","chicago":"Chmelik, Martin. “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.","ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","mla":"Chmelik, Martin. <i>Algorithms for Partially Observable Markov Decision Processes</i>. Institute of Science and Technology Austria, 2016."}},{"_id":"1129","language":[{"iso":"eng"}],"title":"Quantitative analysis of haptotactic cell migration","status":"public","file":[{"creator":"dernst","file_id":"6813","file_name":"Thesis_JSchwarz_final.pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file","checksum":"e3cd6b28f9c5cccb8891855565a2dade","file_size":32044069,"date_updated":"2019-08-13T10:55:35Z","date_created":"2019-08-13T10:55:35Z"},{"date_updated":"2021-02-22T11:43:14Z","date_created":"2021-02-22T11:43:14Z","success":1,"file_size":8396717,"checksum":"c3dbe219acf87eed2f46d21d5cca00de","file_name":"2016_Thesis_JSchwarz.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"9181"}],"ddc":["570"],"date_updated":"2026-04-08T14:28:53Z","publication_status":"published","author":[{"first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"}],"month":"07","abstract":[{"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.","lang":"eng"}],"publist_id":"6231","page":"178","year":"2016","date_created":"2018-12-11T11:50:18Z","oa_version":"Published Version","citation":{"short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 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.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"MiSi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","day":"01","date_published":"2016-07-01T00:00:00Z","OA_place":"publisher","file_date_updated":"2021-02-22T11:43:14Z","type":"dissertation","oa":1,"has_accepted_license":"1","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","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"corr_author":"1"}]