[{"citation":{"mla":"Tarlungeanu, Dora-Clara. <i>The Branched Chain Amino Acids in Autism Spectrum Disorders </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>.","ista":"Tarlungeanu D-C. 2018. The branched chain amino acids in autism spectrum disorders . Institute of Science and Technology Austria.","ieee":"D.-C. Tarlungeanu, “The branched chain amino acids in autism spectrum disorders ,” Institute of Science and Technology Austria, 2018.","chicago":"Tarlungeanu, Dora-Clara. “The Branched Chain Amino Acids in Autism Spectrum Disorders .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>.","apa":"Tarlungeanu, D.-C. (2018). <i>The branched chain amino acids in autism spectrum disorders </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">https://doi.org/10.15479/AT:ISTA:th_992</a>","ama":"Tarlungeanu D-C. The branched chain amino acids in autism spectrum disorders . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_992\">10.15479/AT:ISTA:th_992</a>","short":"D.-C. Tarlungeanu, The Branched Chain Amino Acids in Autism Spectrum Disorders , Institute of Science and Technology Austria, 2018."},"title":"The branched chain amino acids in autism spectrum disorders ","day":"01","alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","first_name":"Dora-Clara","last_name":"Tarlungeanu"}],"related_material":{"record":[{"id":"1183","relation":"part_of_dissertation","status":"public"}]},"project":[{"name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["570","616"],"doi":"10.15479/AT:ISTA:th_992","page":"88","month":"03","date_created":"2018-12-11T11:46:14Z","supervisor":[{"first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GaNo"}],"status":"public","publist_id":"7434","oa_version":"Published Version","year":"2018","has_accepted_license":"1","date_updated":"2023-09-07T12:38:59Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"article_processing_charge":"No","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6217","relation":"source_file","date_created":"2019-04-05T09:19:17Z","embargo_to":"open_access","file_name":"2018_Thesis_Tarlungeanu_source.docx","file_size":43684035,"creator":"dernst","date_updated":"2021-02-11T23:30:15Z","access_level":"closed","checksum":"9f5231c96e0ad945040841a8630232da"},{"date_created":"2019-04-05T09:19:17Z","relation":"main_file","file_id":"6218","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","checksum":"0c33c370aa2010df5c552db57a6d01e9","embargo":"2018-03-15","file_size":30511532,"creator":"dernst","file_name":"2018_Thesis_Tarlungeanu.pdf"}],"_id":"395","date_published":"2018-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. "}],"publication_status":"published","oa":1,"file_date_updated":"2021-02-11T23:30:15Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"992"},{"oa_version":"Published Version","has_accepted_license":"1","year":"2018","publist_id":"7405","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-22T09:20:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","_id":"418","date_published":"2018-01-08T00:00:00Z","abstract":[{"text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion.","lang":"eng"}],"file":[{"checksum":"697fa72ca36fb1b8ceabc133d58a73e5","access_level":"closed","date_updated":"2020-07-14T12:46:24Z","creator":"dernst","file_size":7012495,"file_name":"2018_THESIS_Gschaider-Reichhart_source.docx","date_created":"2019-04-05T09:28:03Z","relation":"source_file","file_id":"6222","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_updated":"2020-07-14T12:46:24Z","access_level":"open_access","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","file_name":"2018_THESIS_Gschaider-Reichhart.pdf","file_size":6355280,"creator":"dernst","date_created":"2019-04-05T09:28:03Z","content_type":"application/pdf","relation":"main_file","file_id":"6223"}],"oa":1,"publication_status":"published","pubrep_id":"913","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:46:24Z","title":"Optical and optogenetic control of proliferation and survival ","citation":{"chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">https://doi.org/10.15479/AT:ISTA:th_913</a>.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","mla":"Gschaider-Reichhart, Eva. <i>Optical and Optogenetic Control of Proliferation and Survival </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">10.15479/AT:ISTA:th_913</a>.","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">10.15479/AT:ISTA:th_913</a>","apa":"Gschaider-Reichhart, E. (2018). <i>Optical and optogenetic control of proliferation and survival </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_913\">https://doi.org/10.15479/AT:ISTA:th_913</a>"},"type":"dissertation","author":[{"full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"}],"alternative_title":["ISTA Thesis"],"day":"08","related_material":{"record":[{"relation":"part_of_dissertation","id":"1441","status":"public"},{"relation":"part_of_dissertation","id":"1678","status":"public"},{"id":"2084","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1028","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:th_913","ddc":["571","570"],"language":[{"iso":"eng"}],"page":"107","supervisor":[{"first_name":"Harald L","full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"date_created":"2018-12-11T11:46:22Z","month":"01","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"HaJa"}]},{"file_date_updated":"2021-02-22T11:52:56Z","oa":1,"publication_status":"published","date_published":"2017-01-12T00:00:00Z","_id":"1127","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."}],"file":[{"date_created":"2019-04-05T08:45:14Z","relation":"main_file","file_id":"6209","content_type":"application/pdf","checksum":"d192c7c6c5ea32c8432437286dc4909e","access_level":"closed","date_updated":"2019-04-05T08:45:14Z","file_size":10285946,"creator":"dernst","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf"},{"content_type":"application/pdf","relation":"main_file","file_id":"9185","date_created":"2021-02-22T11:52:56Z","success":1,"file_name":"2017_Thesis_Prat.pdf","file_size":9802991,"creator":"dernst","checksum":"bab18b52cf98145926042d8ed99fdb3b","date_updated":"2021-02-22T11:52:56Z","access_level":"open_access"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-05-07T11:12:27Z","year":"2017","has_accepted_license":"1","oa_version":"Published Version","publist_id":"6233","status":"public","department":[{"_id":"JiFr"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"}],"date_created":"2018-12-11T11:50:17Z","month":"01","page":"131","ddc":["580"],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"449","relation":"part_of_dissertation","status":"public"}]},"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.","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Prat, Tomas","last_name":"Prat"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"day":"12","title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","citation":{"short":"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.","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.","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."}},{"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"ToHe"}],"status":"public","page":"163","month":"01","date_created":"2018-12-11T11:50:27Z","supervisor":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"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. ","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"related_material":{"record":[{"id":"1093","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1230"},{"id":"1234","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1391"},{"status":"public","id":"1501","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1502"},{"id":"2063","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"2167","status":"public"}]},"language":[{"iso":"eng"}],"ddc":["004","005"],"doi":"10.15479/AT:ISTA:TH_730","ec_funded":1,"citation":{"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>","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>."},"title":"Statistical and logical methods for property checking","day":"02","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Daca","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:44:34Z","pubrep_id":"730","article_processing_charge":"No","file":[{"content_type":"application/pdf","file_id":"4880","relation":"main_file","date_created":"2018-12-12T10:11:26Z","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","creator":"system","file_size":1028586,"date_updated":"2020-07-14T12:44:34Z","access_level":"open_access","checksum":"1406a681cb737508234fde34766be2c2"}],"date_published":"2017-01-02T00:00:00Z","_id":"1155","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T11:58:34Z","publication_identifier":{"issn":["2663-337X"]},"publist_id":"6203","year":"2017","oa_version":"Published Version","has_accepted_license":"1"},{"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","citation":{"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.","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>","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>","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>.","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.","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>."},"alternative_title":["ISTA Thesis"],"author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch"}],"type":"dissertation","day":"27","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. ","related_material":{"record":[{"status":"public","id":"2001","relation":"part_of_dissertation"},{"id":"666","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT:ISTA:th_862","ddc":["571","579"],"language":[{"iso":"eng"}],"page":"113","date_created":"2018-12-11T11:48:40Z","supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach"}],"month":"09","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"ToBo"}],"has_accepted_license":"1","oa_version":"Published Version","year":"2017","publist_id":"6831","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:00:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_published":"2017-09-27T00:00:00Z","_id":"818","abstract":[{"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. ","lang":"eng"}],"file":[{"file_name":"Thesis_KarinMitosch.docx","creator":"dernst","file_size":6331071,"date_updated":"2020-07-14T12:48:09Z","access_level":"closed","checksum":"da3993c5f90f59a8e8623cc31ad501dd","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6210","relation":"source_file","date_created":"2019-04-05T08:48:51Z"},{"content_type":"application/pdf","file_id":"6211","relation":"main_file","date_created":"2019-04-05T08:48:51Z","file_name":"Thesis_KarinMitosch.pdf","creator":"dernst","file_size":9289852,"checksum":"24c3d9e51992f1b721f3df55aa13fcb8","date_updated":"2020-07-14T12:48:09Z","access_level":"open_access"}],"oa":1,"publication_status":"published","pubrep_id":"862","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:09Z"},{"oa":1,"publication_status":"published","pubrep_id":"861","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:09Z","article_processing_charge":"No","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. "}],"_id":"819","date_published":"2017-09-26T00:00:00Z","file":[{"relation":"source_file","file_id":"6199","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-05T07:53:04Z","file_size":18580400,"creator":"dernst","file_name":"2017_Thesis_Pull.docx","access_level":"closed","date_updated":"2020-07-14T12:48:09Z","checksum":"4993cdd5382295758ecc3ecbd2a9aaff"},{"date_created":"2019-04-05T07:53:04Z","content_type":"application/pdf","file_id":"6200","relation":"main_file","checksum":"ee2e3ebb5b53c154c866f5b052b25153","date_updated":"2020-07-14T12:48:09Z","access_level":"open_access","file_name":"2017_Thesis_Pull.pdf","creator":"dernst","file_size":14400681}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-28T11:31:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","year":"2017","oa_version":"Published Version","publist_id":"6830","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"SyCr"}],"page":"122","date_created":"2018-12-11T11:48:40Z","supervisor":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia M","full_name":"Cremer, Sylvia M"}],"month":"09","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. ","related_material":{"record":[{"status":"public","id":"616","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"806","status":"public"},{"relation":"part_of_dissertation","id":"734","status":"public"},{"relation":"part_of_dissertation","id":"732","status":"public"}]},"doi":"10.15479/AT:ISTA:th_861","ddc":["576","577","578","579","590","592"],"language":[{"iso":"eng"}],"title":"Disease defence in garden ants","citation":{"ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","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>.","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>.","short":"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>","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>"},"alternative_title":["ISTA Thesis"],"author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull"}],"type":"dissertation","day":"26"},{"page":"87","date_created":"2018-12-11T11:48:41Z","supervisor":[{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"month":"08","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"JoBo"}],"title":"The lac operon in the wild","ec_funded":1,"citation":{"short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","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>","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>","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>.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","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>."},"alternative_title":["ISTA Thesis"],"author":[{"first_name":"Fabienne","full_name":"Jesse, Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"25","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. ","project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"ddc":["576","577","579"],"doi":"10.15479/AT:ISTA:th_857","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2017-08-25T00:00:00Z","_id":"820","abstract":[{"lang":"eng","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."}],"file":[{"relation":"main_file","file_id":"5252","content_type":"application/pdf","date_created":"2018-12-12T10:17:00Z","creator":"system","file_size":3417773,"file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c"},{"checksum":"fc87d7d72fce52824a3ae7dcad0413a8","date_updated":"2020-07-14T12:48:10Z","access_level":"closed","file_name":"2017_thesis_Jesse_source.tex","file_size":215899,"creator":"dernst","date_created":"2019-04-05T08:51:59Z","content_type":"application/x-tex","relation":"source_file","file_id":"6212"}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"857","file_date_updated":"2020-07-14T12:48:10Z","oa_version":"Published Version","year":"2017","has_accepted_license":"1","publist_id":"6829","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:01:21Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"KrCh"}],"page":"418","date_created":"2018-12-11T11:48:41Z","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"month":"08","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.","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"1071","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1437","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"status":"public","relation":"part_of_dissertation","id":"1604"},{"relation":"part_of_dissertation","id":"1607","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1714"}]},"doi":"10.15479/AT:ISTA:th_854","ddc":["000"],"language":[{"iso":"eng"}],"title":"Algorithmic advances in program analysis and their applications","ec_funded":1,"citation":{"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>.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","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>.","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>","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>","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017."},"alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"day":"09","oa":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_status":"published","pubrep_id":"854","tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)"},"file_date_updated":"2020-07-14T12:48:10Z","article_processing_charge":"No","_id":"821","date_published":"2017-08-09T00:00:00Z","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."}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_size":4103115,"creator":"system","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","date_created":"2018-12-12T10:11:44Z","relation":"main_file","file_id":"4900","content_type":"application/pdf"},{"date_created":"2019-04-05T07:59:31Z","relation":"source_file","file_id":"6201","content_type":"application/zip","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","access_level":"closed","date_updated":"2020-07-14T12:48:10Z","creator":"dernst","file_size":14744374,"file_name":"2017_thesis_Pavlogiannis.zip"}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:01:59Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","oa_version":"Published Version","year":"2017","publist_id":"6828"},{"page":"93","date_created":"2018-12-11T11:48:46Z","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"month":"08","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"JoCs"}],"title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","citation":{"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>","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>","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>.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","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>."},"alternative_title":["ISTA Thesis"],"author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Haibing","full_name":"Xu, Haibing"}],"type":"dissertation","day":"23","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. ","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5828"}]},"doi":"10.15479/AT:ISTA:th_858","ddc":["571"],"language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"lang":"eng","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. "}],"_id":"837","date_published":"2017-08-23T00:00:00Z","file":[{"date_created":"2019-04-05T08:59:51Z","relation":"source_file","file_id":"6213","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2020-07-14T12:48:12Z","checksum":"f11925fbbce31e495124b6bc4f10573c","file_size":3589490,"creator":"dernst","file_name":"2017_Xu_Haibing_Thesis_Source.docx"},{"file_name":"2017_Xu_Thesis_IST.pdf","creator":"dernst","file_size":11668613,"checksum":"ffb10749a537d615fab1ef0937ccb157","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"6214","date_created":"2019-04-05T08:59:51Z"}],"oa":1,"publication_status":"published","pubrep_id":"858","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:12Z","oa_version":"Published Version","has_accepted_license":"1","year":"2017","publist_id":"6811","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T12:06:38Z"},{"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:02:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","has_accepted_license":"1","oa_version":"Published Version","publist_id":"6810","pubrep_id":"828","file_date_updated":"2020-07-14T12:48:12Z","oa":1,"publication_status":"published","_id":"838","date_published":"2017-06-26T00:00:00Z","abstract":[{"lang":"eng","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. "}],"file":[{"checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","creator":"system","file_size":847400,"date_created":"2018-12-12T10:10:13Z","content_type":"application/pdf","relation":"main_file","file_id":"4799"},{"access_level":"closed","date_updated":"2020-07-14T12:48:12Z","checksum":"3462101745ce8ad199c2d0f75dae4a7e","creator":"dernst","file_size":26054879,"file_name":"2017_Thesis_Rybar_source.zip","date_created":"2019-04-05T08:24:11Z","relation":"source_file","file_id":"6202","content_type":"application/zip"}],"article_processing_charge":"No","doi":"10.15479/AT:ISTA:th_828","ddc":["000"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2082"},{"id":"6196","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"author":[{"last_name":"Rybar","first_name":"Michal","full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"26","title":"(The exact security of) Message authentication codes","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>","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>","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.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria."},"status":"public","department":[{"_id":"KrPi"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:48:46Z","month":"06","page":"86"},{"file":[{"checksum":"6c1ae8c90bfaba5e089417fefbc4a272","date_updated":"2020-07-14T12:48:13Z","access_level":"open_access","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","file_size":14596191,"creator":"system","date_created":"2018-12-12T10:14:46Z","content_type":"application/pdf","relation":"main_file","file_id":"5100"},{"checksum":"421672f68d563b029869c5cf1713f919","access_level":"closed","date_updated":"2020-07-14T12:48:13Z","file_size":15060566,"creator":"dernst","file_name":"2017_thesis_Hahn_source.zip","date_created":"2019-04-05T08:40:30Z","file_id":"6207","relation":"source_file","content_type":"application/zip"}],"_id":"839","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. "}],"date_published":"2017-08-14T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:13Z","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"pubrep_id":"855","license":"https://creativecommons.org/licenses/by-sa/4.0/","publication_status":"published","oa":1,"publist_id":"6809","oa_version":"Published Version","year":"2017","has_accepted_license":"1","date_updated":"2024-02-21T13:48:02Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"08","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"date_created":"2018-12-11T11:48:47Z","page":"124","department":[{"_id":"ChWo"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","day":"14","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn","full_name":"Hahn, David","first_name":"David"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"citation":{"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>.","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>.","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.","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>","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>","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017."},"ec_funded":1,"title":"Brittle fracture simulation with boundary elements for computer graphics","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_855","ddc":["004","005","006","531","621"],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1362"},{"status":"public","id":"1633","relation":"part_of_dissertation"},{"status":"public","id":"5568","relation":"popular_science"}]},"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"},{"date_updated":"2023-09-15T12:04:56Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"publist_id":"7711","year":"2017","oa_version":"Published Version","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:24Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"916","publication_status":"published","oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"4710","date_created":"2018-12-12T10:08:48Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","creator":"system","file_size":18569590,"checksum":"33cfb59674e91f82e3738396d3fb3776","date_updated":"2020-07-14T12:45:24Z","access_level":"open_access"},{"file_name":"2017_Pleska_Maros_Thesis.docx","creator":"dernst","file_size":2801649,"date_updated":"2020-07-14T12:45:24Z","access_level":"closed","checksum":"dcc239968decb233e7f98cf1083d8c26","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6204","relation":"source_file","date_created":"2019-04-05T08:33:14Z"}],"_id":"202","abstract":[{"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.","lang":"eng"}],"date_published":"2017-10-01T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_916","ddc":["576","579"],"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"related_material":{"record":[{"id":"1243","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"457"}]},"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","day":"01","type":"dissertation","author":[{"first_name":"Maros","full_name":"Pleska, Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479"}],"alternative_title":["ISTA Thesis"],"citation":{"ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","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>.","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>.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","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>","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>"},"title":"Biology of restriction-modification systems at the single-cell and population level","department":[{"_id":"CaGu"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","month":"10","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C"}],"date_created":"2018-12-11T11:45:10Z","page":"126"},{"article_processing_charge":"No","file":[{"date_created":"2019-04-09T14:54:51Z","content_type":"application/pdf","relation":"main_file","file_id":"6289","checksum":"ece7e598a2f060b263c2febf7f3fe7f9","date_updated":"2020-07-14T12:47:26Z","access_level":"open_access","file_name":"2017_Thesis_Nikitenko.pdf","file_size":2324870,"creator":"dernst"},{"creator":"dernst","file_size":2863219,"file_name":"2017_Thesis_Nikitenko_source.zip","access_level":"closed","date_updated":"2020-07-14T12:47:26Z","checksum":"99b7ad76e317efd447af60f91e29b49b","relation":"source_file","file_id":"6290","content_type":"application/zip","date_created":"2019-04-09T14:54:51Z"}],"date_published":"2017-10-27T00:00:00Z","_id":"6287","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."}],"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:26Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"873","has_accepted_license":"1","year":"2017","oa_version":"Published Version","date_updated":"2023-09-15T12:10:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"page":"86","month":"10","supervisor":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-04-09T15:04:32Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"HeEd"}],"status":"public","citation":{"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>.","ieee":"A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017.","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria.","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>.","short":"A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017.","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>","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>"},"title":"Discrete Morse theory for random complexes ","day":"27","type":"dissertation","author":[{"last_name":"Nikitenko","full_name":"Nikitenko, Anton","first_name":"Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"718","relation":"part_of_dissertation"},{"status":"public","id":"5678","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"87","status":"public"}]},"language":[{"iso":"eng"}],"ddc":["514","516","519"],"doi":"10.15479/AT:ISTA:th_873"},{"file_date_updated":"2021-02-22T13:45:59Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","publication_status":"published","publisher":"Institute of Science and Technology Austria","oa":1,"degree_awarded":"PhD","file":[{"file_id":"6292","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-09T15:15:32Z","creator":"dernst","file_size":3025175,"file_name":"thesis_pavel_payne_final_w_signature_page.pdf","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","access_level":"closed","date_updated":"2020-07-14T12:47:27Z"},{"file_name":"2017_Payne_Thesis.pdf","creator":"dernst","file_size":3111536,"checksum":"af531e921a7f64a9e0af4cd8783b2226","date_updated":"2021-02-22T13:45:59Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"9187","date_created":"2021-02-22T13:45:59Z","success":1}],"month":"02","_id":"6291","date_created":"2019-04-09T15:16:45Z","date_published":"2017-02-01T00:00:00Z","abstract":[{"lang":"eng","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."}],"supervisor":[{"first_name":"Jonathan P","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"page":"83","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T12:00:00Z","ddc":["570"],"publication_identifier":{"issn":["2663-337X"]},"day":"01","has_accepted_license":"1","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"year":"2017","type":"dissertation","author":[{"last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"P. Payne, 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.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. <i>Bacterial Herd and Social Immunity to Phages</i>. Institute of Science and Technology Austria, 2017."},"title":"Bacterial herd and social immunity to phages"},{"article_processing_charge":"No","_id":"938","date_published":"2017-06-02T00:00:00Z","abstract":[{"lang":"eng","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."}],"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6215","relation":"source_file","date_created":"2019-04-05T09:03:20Z","file_name":"2017_Adamowski-Thesis_Source.docx","file_size":46903863,"creator":"dernst","checksum":"193425764d9aaaed3ac57062a867b315","date_updated":"2020-07-14T12:48:15Z","access_level":"closed"},{"access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","checksum":"df5ab01be81f821e1b958596a1ec8d21","creator":"dernst","file_size":8698888,"file_name":"2017_Adamowski-Thesis.pdf","date_created":"2019-04-05T09:03:19Z","relation":"main_file","file_id":"6216","content_type":"application/pdf"}],"oa":1,"publication_status":"published","pubrep_id":"842","file_date_updated":"2020-07-14T12:48:15Z","year":"2017","has_accepted_license":"1","oa_version":"Published Version","publist_id":"6483","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:06:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"117","supervisor":[{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_created":"2018-12-11T11:49:18Z","month":"06","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"JiFr"}],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","citation":{"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.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","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>.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","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>","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>"},"type":"dissertation","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek","first_name":"Maciek"}],"alternative_title":["ISTA Thesis"],"day":"02","related_material":{"record":[{"status":"public","id":"1591","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:th_842","ddc":["581","583","580"],"language":[{"iso":"eng"}]},{"page":"109","month":"03","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"date_created":"2018-12-11T11:49:25Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"CaHe"}],"status":"public","citation":{"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>","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>.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","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>."},"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","day":"01","author":[{"last_name":"Barone","first_name":"Vanessa","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1100"},{"relation":"part_of_dissertation","id":"1537","status":"public"},{"status":"public","id":"1912","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"2926","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"3246"},{"status":"public","relation":"part_of_dissertation","id":"676"},{"status":"public","id":"735","relation":"part_of_dissertation"}]},"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!","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_825","ddc":["570","590"],"article_processing_charge":"No","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6205","relation":"source_file","date_created":"2019-04-05T08:36:52Z","file_name":"2017_Barone_thesis_final.docx","creator":"dernst","file_size":14497822,"date_updated":"2020-07-14T12:48:16Z","access_level":"closed","checksum":"242f88c87f2cf267bf05049fa26a687b"},{"date_created":"2019-04-05T08:36:52Z","content_type":"application/pdf","relation":"main_file","file_id":"6206","checksum":"ba5b0613ed8bade73a409acdd880fb8a","date_updated":"2020-07-14T12:48:16Z","access_level":"open_access","file_name":"2017_Barone_thesis_.pdf","creator":"dernst","file_size":14995941}],"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."}],"_id":"961","date_published":"2017-03-01T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:16Z","pubrep_id":"825","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publist_id":"6444","oa_version":"Published Version","year":"2017","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-27T14:16:45Z","publication_identifier":{"issn":["2663-337X"]}},{"oa":1,"publication_status":"published","pubrep_id":"815","file_date_updated":"2020-07-14T12:48:18Z","article_processing_charge":"No","_id":"992","date_published":"2017-05-01T00:00:00Z","abstract":[{"lang":"eng","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)."}],"file":[{"date_created":"2018-12-12T10:07:55Z","content_type":"application/pdf","relation":"main_file","file_id":"4654","date_updated":"2020-07-14T12:48:18Z","access_level":"open_access","checksum":"81761fb939acb7585c36629f765b4373","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","file_size":786145,"creator":"system"},{"date_updated":"2020-07-14T12:48:18Z","access_level":"closed","checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","file_name":"2017_Thesis_Rolinek_source.zip","file_size":5936337,"creator":"dernst","date_created":"2019-04-05T08:43:24Z","content_type":"application/zip","file_id":"6208","relation":"source_file"}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:05:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","has_accepted_license":"1","oa_version":"Published Version","publist_id":"6407","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"VlKo"}],"page":"97","supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:49:35Z","month":"05","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","ddc":["004"],"doi":"10.15479/AT:ISTA:th_815","language":[{"iso":"eng"}],"title":"Complexity of constraint satisfaction","citation":{"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>.","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>.","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","ieee":"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>","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>","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017."},"ec_funded":1,"author":[{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"day":"01"},{"publist_id":"6239","oa_version":"Published Version","has_accepted_license":"1","year":"2016","date_updated":"2023-09-07T11:42:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_updated":"2019-08-13T11:17:50Z","access_level":"closed","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_name":"PhDThesis_HandeAcar_1230.pdf","file_size":3682711,"creator":"dernst","date_created":"2019-08-13T11:17:50Z","content_type":"application/pdf","file_id":"6814","relation":"main_file"},{"date_created":"2021-02-22T11:51:13Z","success":1,"relation":"main_file","file_id":"9184","content_type":"application/pdf","checksum":"94bbbc754c36115bf37f8fc11fad43c4","access_level":"open_access","date_updated":"2021-02-22T11:51:13Z","creator":"dernst","file_size":3682711,"file_name":"2016_Thesis_HandeAcar.pdf"}],"_id":"1121","date_published":"2016-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments."}],"article_processing_charge":"No","file_date_updated":"2021-02-22T11:51:13Z","publication_status":"published","oa":1,"day":"01","author":[{"orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","full_name":"Acar, Hande","first_name":"Hande"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"citation":{"short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016."},"ec_funded":1,"title":"Selective barriers to horizontal gene transfer","language":[{"iso":"eng"}],"ddc":["570"],"project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","month":"12","supervisor":[{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P"}],"date_created":"2018-12-11T11:50:16Z","page":"75","department":[{"_id":"JoBo"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD"},{"file_date_updated":"2018-12-12T10:13:02Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"file":[{"file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","creator":"system","file_size":13869345,"date_updated":"2018-12-12T10:13:02Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4982","date_created":"2018-12-12T10:13:02Z"}],"date_published":"2016-07-15T00:00:00Z","_id":"1122","abstract":[{"lang":"eng","text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed."}],"article_processing_charge":"No","date_updated":"2024-02-21T13:50:48Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"publist_id":"6238","oa_version":"Published Version","year":"2016","has_accepted_license":"1","department":[{"_id":"ChWo"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","month":"07","date_created":"2018-12-11T11:50:16Z","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"page":"114","language":[{"iso":"eng"}],"ddc":["004","005","006","532","621"],"doi":"10.15479/AT:ISTA:th_640","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","related_material":{"record":[{"status":"public","relation":"other","id":"5558"}]},"day":"15","alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen"}],"citation":{"short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>","apa":"Bojsen-Hansen, M. (2016). <i>Tracking, correcting and absorbing water surface waves</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>."},"title":"Tracking, correcting and absorbing water surface waves"},{"publication_status":"published","oa":1,"file_date_updated":"2021-02-22T11:36:34Z","article_processing_charge":"No","file":[{"file_id":"6809","relation":"main_file","content_type":"application/pdf","date_created":"2019-08-13T08:45:27Z","file_size":2227916,"creator":"dernst","file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","access_level":"closed","date_updated":"2019-08-13T08:45:27Z","checksum":"2d140cc924cd1b764544906fc22684ef"},{"file_name":"2016_Mabillard_Thesis.pdf","file_size":2227916,"creator":"dernst","checksum":"2d140cc924cd1b764544906fc22684ef","date_updated":"2021-02-22T11:36:34Z","access_level":"open_access","content_type":"application/pdf","file_id":"9178","relation":"main_file","date_created":"2021-02-22T11:36:34Z","success":1}],"_id":"1123","date_published":"2016-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems  in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K  can be mapped into Rd  without triple, quadruple, or, more generally, r-fold points  (image points with at least r  distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd  that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint  simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction  for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK  = (r ≥ 1)k  and d  = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign  can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN  to Rd  without r-Tverberg points when r not a prime power  and\r\nN  = (d  + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K  = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle&quot; and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r  + 1 and r  not a prime power, by a reduction1  to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r  not a prime power.     "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T11:56:28Z","publication_identifier":{"issn":["2663-337X"]},"publist_id":"6237","year":"2016","has_accepted_license":"1","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"UlWa"}],"status":"public","page":"55","month":"08","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"date_created":"2018-12-11T11:50:16Z","related_material":{"record":[{"status":"public","id":"2159","relation":"part_of_dissertation"}]},"acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","language":[{"iso":"eng"}],"ddc":["500"],"citation":{"ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","mla":"Mabillard, Isaac. <i>Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture</i>. Institute of Science and Technology Austria, 2016.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). <i>Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture</i>. Institute of Science and Technology Austria.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016."},"title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","day":"01","author":[{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","full_name":"Mabillard, Isaac","first_name":"Isaac"}],"type":"dissertation","alternative_title":["ISTA Thesis"]}]