[{"type":"dissertation","date_created":"2019-04-09T15:16:45Z","oa_version":"Published Version","oa":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"page":"83","date_published":"2017-02-01T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"citation":{"ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","mla":"Payne, Pavel. <i>Bacterial Herd and Social Immunity to Phages</i>. Institute of Science and Technology Austria, 2017.","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."},"date_updated":"2026-04-08T14:16:28Z","_id":"6291","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."}],"year":"2017","article_processing_charge":"No","author":[{"first_name":"Pavel","last_name":"Payne","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Bacterial herd and social immunity to phages","corr_author":"1","OA_place":"publisher","month":"02","file_date_updated":"2021-02-22T13:45:59Z","ddc":["570"],"supervisor":[{"first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","file":[{"relation":"main_file","date_created":"2019-04-09T15:15:32Z","file_id":"6292","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","content_type":"application/pdf","date_updated":"2020-07-14T12:47:27Z","creator":"dernst","access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","file_size":3025175},{"date_updated":"2021-02-22T13:45:59Z","creator":"dernst","content_type":"application/pdf","checksum":"af531e921a7f64a9e0af4cd8783b2226","file_size":3111536,"access_level":"open_access","file_name":"2017_Payne_Thesis.pdf","success":1,"relation":"main_file","date_created":"2021-02-22T13:45:59Z","file_id":"9187"}],"publication_identifier":{"issn":["2663-337X"]},"day":"01","status":"public"},{"status":"public","day":"23","publication_identifier":{"issn":["2663-337X"]},"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:12Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"f11925fbbce31e495124b6bc4f10573c","file_size":3589490,"access_level":"closed","file_name":"2017_Xu_Haibing_Thesis_Source.docx","relation":"source_file","date_created":"2019-04-05T08:59:51Z","file_id":"6213"},{"date_updated":"2020-07-14T12:48:12Z","creator":"dernst","checksum":"ffb10749a537d615fab1ef0937ccb157","content_type":"application/pdf","file_size":11668613,"access_level":"open_access","file_name":"2017_Xu_Thesis_IST.pdf","relation":"main_file","date_created":"2019-04-05T08:59:51Z","file_id":"6214"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","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. ","supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"ddc":["571"],"pubrep_id":"858","file_date_updated":"2020-07-14T12:48:12Z","doi":"10.15479/AT:ISTA:th_858","license":"https://creativecommons.org/licenses/by/4.0/","month":"08","publist_id":"6811","corr_author":"1","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Xu","first_name":"Haibing","full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5828"}]},"article_processing_charge":"No","year":"2017","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_updated":"2026-04-08T14:18:55Z","date_published":"2017-08-23T00:00:00Z","department":[{"_id":"JoCs"}],"citation":{"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>.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","ieee":"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>","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017."},"page":"93","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"oa_version":"Published Version","date_created":"2018-12-11T11:48:46Z","type":"dissertation"},{"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_size":847400,"access_level":"open_access","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","date_updated":"2020-07-14T12:48:12Z","creator":"system","content_type":"application/pdf","checksum":"ff8639ec4bded6186f44c7bd3ee26804","file_id":"4799","date_created":"2018-12-12T10:10:13Z","relation":"main_file"},{"file_id":"6202","date_created":"2019-04-05T08:24:11Z","relation":"source_file","file_size":26054879,"access_level":"closed","file_name":"2017_Thesis_Rybar_source.zip","date_updated":"2020-07-14T12:48:12Z","creator":"dernst","checksum":"3462101745ce8ad199c2d0f75dae4a7e","content_type":"application/zip"}],"status":"public","day":"26","degree_awarded":"PhD","publication_status":"published","publisher":"Institute of Science and Technology Austria","ddc":["000"],"pubrep_id":"828","file_date_updated":"2020-07-14T12:48:12Z","doi":"10.15479/AT:ISTA:th_828","month":"06","corr_author":"1","OA_place":"publisher","publist_id":"6810","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"(The exact security of) Message authentication codes","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"2082","status":"public","relation":"part_of_dissertation"},{"id":"6196","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"article_processing_charge":"No","year":"2017","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"838","date_updated":"2026-04-08T14:18:39Z","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. "}],"page":"86","citation":{"ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","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>","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>.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","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>."},"date_published":"2017-06-26T00:00:00Z","department":[{"_id":"KrPi"}],"oa":1,"type":"dissertation","oa_version":"Published Version","date_created":"2018-12-11T11:48:46Z"},{"oa":1,"issue":"2","type":"journal_article","date_created":"2019-04-04T13:48:23Z","oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2017-02-03T00:00:00Z","page":"145-161","department":[{"_id":"KrPi"}],"citation":{"ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. 2017;2016(2):145-161. doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum, 2017. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>.","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161.","mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>.","apa":"Gazi, P., Pietrzak, K. Z., &#38; Rybar, M. (2017). The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>"},"_id":"6196","date_updated":"2026-04-08T14:18:39Z","abstract":[{"text":"PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of  Ο(σ2/2n), while the currently best bound is  Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"838","status":"public"}]},"author":[{"last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal"}],"intvolume":"      2016","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The exact security of PMAC","ec_funded":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}],"doi":"10.13154/TOSC.V2016.I2.145-161","file_date_updated":"2020-07-14T12:47:24Z","month":"02","ddc":["000"],"quality_controlled":"1","file":[{"file_id":"6197","relation":"main_file","date_created":"2019-04-04T13:53:58Z","file_size":597335,"file_name":"2017_IACR_Gazi.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:24Z","creator":"dernst","checksum":"f23161d685dd957ae8d7274132999684","content_type":"application/pdf"}],"publication_identifier":{"eissn":["2519-173X"]},"day":"03","status":"public","publisher":"Ruhr University Bochum","publication_status":"published","publication":"IACR Transactions on Symmetric Cryptology","volume":2016,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"publication_status":"published","publisher":"BioMed Central","volume":17,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"BMC Evolutionary Biology","publication_identifier":{"issn":["1471-2148"]},"file":[{"date_created":"2018-12-12T10:17:18Z","relation":"main_file","file_id":"5271","date_updated":"2020-07-14T12:47:55Z","creator":"system","checksum":"3e24a2cfd48f49f7b3643d08d30fb480","content_type":"application/pdf","file_size":949857,"access_level":"open_access","file_name":"IST-2017-882-v1+1_12862_2017_Article_1062.pdf"}],"status":"public","day":"13","external_id":{"isi":["000412816800001"]},"ddc":["576","592"],"quality_controlled":"1","month":"10","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:47:55Z","pubrep_id":"882","doi":"10.1186/s12862-017-1062-4","corr_author":"1","publist_id":"6937","ec_funded":1,"scopus_import":"1","title":"Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","year":"2017","related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"article_type":"original","intvolume":"        17","author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"732","date_updated":"2026-04-08T14:19:10Z","abstract":[{"text":"Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens.","lang":"eng"}],"department":[{"_id":"SyCr"}],"date_published":"2017-10-13T00:00:00Z","citation":{"ieee":"C. Pull and S. Cremer, “Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour,” <i>BMC Evolutionary Biology</i>, vol. 17, no. 1. BioMed Central, 2017.","ama":"Pull C, Cremer S. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. <i>BMC Evolutionary Biology</i>. 2017;17(1). doi:<a href=\"https://doi.org/10.1186/s12862-017-1062-4\">10.1186/s12862-017-1062-4</a>","chicago":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2017. <a href=\"https://doi.org/10.1186/s12862-017-1062-4\">https://doi.org/10.1186/s12862-017-1062-4</a>.","ista":"Pull C, Cremer S. 2017. Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. BMC Evolutionary Biology. 17(1), 219.","apa":"Pull, C., &#38; Cremer, S. (2017). Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12862-017-1062-4\">https://doi.org/10.1186/s12862-017-1062-4</a>","mla":"Pull, Christopher, and Sylvia Cremer. “Co-Founding Ant Queens Prevent Disease by Performing Prophylactic Undertaking Behaviour.” <i>BMC Evolutionary Biology</i>, vol. 17, no. 1, 219, BioMed Central, 2017, doi:<a href=\"https://doi.org/10.1186/s12862-017-1062-4\">10.1186/s12862-017-1062-4</a>.","short":"C. Pull, S. Cremer, BMC Evolutionary Biology 17 (2017)."},"article_number":"219","type":"journal_article","date_created":"2018-12-11T11:48:12Z","oa_version":"Published Version","oa":1,"isi":1,"issue":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Discrete Morse theory for random complexes ","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","orcid":"0000-0002-0659-3201","first_name":"Anton"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"87"},{"relation":"part_of_dissertation","id":"5678","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"718"}]},"year":"2017","article_processing_charge":"No","department":[{"_id":"HeEd"}],"citation":{"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>","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.","ieee":"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>","chicago":"Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_873\">https://doi.org/10.15479/AT:ISTA:th_873</a>.","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria."},"page":"86","date_published":"2017-10-27T00:00:00Z","_id":"6287","date_updated":"2026-04-08T14:19:31Z","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_created":"2019-04-09T15:04:32Z","type":"dissertation","day":"27","status":"public","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:26Z","content_type":"application/pdf","checksum":"ece7e598a2f060b263c2febf7f3fe7f9","file_size":2324870,"access_level":"open_access","file_name":"2017_Thesis_Nikitenko.pdf","date_created":"2019-04-09T14:54:51Z","relation":"main_file","file_id":"6289"},{"relation":"source_file","date_created":"2019-04-09T14:54:51Z","file_id":"6290","creator":"dernst","date_updated":"2020-07-14T12:47:26Z","checksum":"99b7ad76e317efd447af60f91e29b49b","content_type":"application/zip","file_size":2863219,"access_level":"closed","file_name":"2017_Thesis_Nikitenko_source.zip"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","ddc":["514","516","519"],"supervisor":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:th_873","file_date_updated":"2020-07-14T12:47:26Z","pubrep_id":"873","month":"10","OA_place":"publisher","corr_author":"1"},{"publisher":"Cambridge University Press","publication_status":"published","publication":"Advances in Applied Probability","volume":49,"arxiv":1,"publication_identifier":{"issn":["0001-8678"]},"day":"01","status":"public","external_id":{"isi":["000416417500004"],"arxiv":["1607.05915"]},"quality_controlled":"1","month":"09","project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"doi":"10.1017/apr.2017.20","publist_id":"6962","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.05915","open_access":"1"}],"scopus_import":"1","title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2017","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"6287","relation":"dissertation_contains"}]},"intvolume":"        49","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"first_name":"Anton","orcid":"0000-0002-0659-3201","last_name":"Nikitenko","full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reitzner","first_name":"Matthias","full_name":"Reitzner, Matthias"}],"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"date_published":"2017-09-01T00:00:00Z","citation":{"apa":"Edelsbrunner, H., Nikitenko, A., &#38; Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>","short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","mla":"Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>.","ieee":"H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” <i>Advances in Applied Probability</i>, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017.","ama":"Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. <i>Advances in Applied Probability</i>. 2017;49(3):745-767. doi:<a href=\"https://doi.org/10.1017/apr.2017.20\">10.1017/apr.2017.20</a>","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” <i>Advances in Applied Probability</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/apr.2017.20\">https://doi.org/10.1017/apr.2017.20</a>.","ista":"Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767."},"page":"745 - 767","_id":"718","date_updated":"2026-04-08T14:19:30Z","abstract":[{"lang":"eng","text":"Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4."}],"type":"journal_article","oa_version":"Preprint","date_created":"2018-12-11T11:48:07Z","oa":1,"isi":1,"issue":"3"},{"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5568"},{"relation":"part_of_dissertation","status":"public","id":"1362"},{"relation":"part_of_dissertation","id":"1633","status":"public"}]},"author":[{"full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn","first_name":"David"}],"year":"2017","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Brittle fracture simulation with boundary elements for computer graphics","alternative_title":["ISTA Thesis"],"oa":1,"type":"dissertation","oa_version":"Published Version","date_created":"2018-12-11T11:48:47Z","has_accepted_license":"1","language":[{"iso":"eng"}],"citation":{"apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","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.","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>","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017."},"department":[{"_id":"ChWo"}],"date_published":"2017-08-14T00:00:00Z","page":"124","_id":"839","date_updated":"2026-04-08T14:20:16Z","abstract":[{"text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ","lang":"eng"}],"ddc":["004","005","006","531","621"],"supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"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","file":[{"date_created":"2018-12-12T10:14:46Z","relation":"main_file","file_id":"5100","creator":"system","date_updated":"2020-07-14T12:48:13Z","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","content_type":"application/pdf","file_size":14596191,"access_level":"open_access","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf"},{"relation":"source_file","date_created":"2019-04-05T08:40:30Z","file_id":"6207","date_updated":"2020-07-14T12:48:13Z","creator":"dernst","checksum":"421672f68d563b029869c5cf1713f919","content_type":"application/zip","file_size":15060566,"access_level":"closed","file_name":"2017_thesis_Hahn_source.zip"}],"publication_identifier":{"issn":["2663-337X"]},"day":"14","status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"ec_funded":1,"OA_place":"publisher","corr_author":"1","publist_id":"6809","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"doi":"10.15479/AT:ISTA:th_855","pubrep_id":"855","file_date_updated":"2020-07-14T12:48:13Z","month":"08","license":"https://creativecommons.org/licenses/by-sa/4.0/"},{"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","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"ddc":["576","579"],"publication_identifier":{"issn":["2663-337X"]},"file":[{"content_type":"application/pdf","checksum":"33cfb59674e91f82e3738396d3fb3776","creator":"system","date_updated":"2020-07-14T12:45:24Z","access_level":"open_access","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","file_size":18569590,"relation":"main_file","date_created":"2018-12-12T10:08:48Z","file_id":"4710"},{"creator":"dernst","date_updated":"2020-07-14T12:45:24Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"dcc239968decb233e7f98cf1083d8c26","file_size":2801649,"file_name":"2017_Pleska_Maros_Thesis.docx","access_level":"closed","relation":"source_file","date_created":"2019-04-05T08:33:14Z","file_id":"6204"}],"status":"public","day":"01","degree_awarded":"PhD","publication_status":"published","publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","OA_place":"publisher","publist_id":"7711","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"}],"file_date_updated":"2020-07-14T12:45:24Z","pubrep_id":"916","doi":"10.15479/AT:ISTA:th_916","month":"10","related_material":{"record":[{"id":"457","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"relation":"part_of_dissertation","id":"1243","status":"public"}]},"author":[{"first_name":"Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"}],"article_processing_charge":"No","year":"2017","title":"Biology of restriction-modification systems at the single-cell and population level","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"oa":1,"type":"dissertation","oa_version":"Published Version","date_created":"2018-12-11T11:45:10Z","language":[{"iso":"eng"}],"has_accepted_license":"1","_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_updated":"2026-04-08T14:19:44Z","page":"126","citation":{"ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","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>.","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>","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>"},"date_published":"2017-10-01T00:00:00Z","department":[{"_id":"CaGu"}]},{"pmid":1,"day":"01","status":"public","publication_identifier":{"issn":["1744-9561"]},"publication":"Biology Letters","volume":13,"publisher":"The Royal Society","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["29237814"],"isi":["000418695400012"]},"acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","doi":"10.1098/rsbl.2017.0646","project":[{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","grant_number":"RGY0079/2011"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210"}],"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2017.0646"}],"publist_id":"7253","corr_author":"1","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","intvolume":"        13","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","first_name":"Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"article_type":"original","related_material":{"record":[{"id":"9847","status":"public","relation":"research_data"},{"status":"public","id":"202","relation":"dissertation_contains"}]},"year":"2017","article_processing_charge":"No","date_published":"2017-12-01T00:00:00Z","citation":{"mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","apa":"Pleska, M., &#38; Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>."},"department":[{"_id":"CaGu"}],"_id":"561","abstract":[{"text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.","lang":"eng"}],"date_updated":"2026-04-08T14:19:43Z","language":[{"iso":"eng"}],"issue":"12","oa":1,"isi":1,"date_created":"2018-12-11T11:47:11Z","oa_version":"Published Version","type":"journal_article","article_number":"20170646"},{"author":[{"full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn","first_name":"David"}],"related_material":{"record":[{"status":"public","id":"839","relation":"research_paper"}]},"ddc":["004"],"year":"2017","keyword":["Boundary elements","brittle fracture","computer graphics","fracture simulation"],"article_processing_charge":"No","day":"16","title":"Source codes: Brittle fracture simulation with boundary elements for computer graphics","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":199353471,"access_level":"open_access","file_name":"IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip","creator":"system","date_updated":"2020-07-14T12:47:04Z","content_type":"application/zip","checksum":"2323a755842a3399cbc47d76545fc9a0","file_id":"5615","relation":"main_file","date_created":"2018-12-12T13:02:57Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"datarep_id":"73","publisher":"Institute of Science and Technology Austria","ec_funded":1,"oa":1,"oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","type":"research_data","doi":"10.15479/AT:ISTA:73","file_date_updated":"2020-07-14T12:47:04Z","project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"D. Hahn, “Source codes: Brittle fracture simulation with boundary elements for computer graphics.” Institute of Science and Technology Austria, 2017.","ama":"Hahn D. Source codes: Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:73\">10.15479/AT:ISTA:73</a>","ista":"Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements for computer graphics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:73\">10.15479/AT:ISTA:73</a>.","chicago":"Hahn, David. “Source Codes: 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:73\">https://doi.org/10.15479/AT:ISTA:73</a>.","short":"D. Hahn, (2017).","mla":"Hahn, David. <i>Source Codes: 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:73\">10.15479/AT:ISTA:73</a>.","apa":"Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:73\">https://doi.org/10.15479/AT:ISTA:73</a>"},"department":[{"_id":"ChWo"}],"date_published":"2017-08-16T00:00:00Z","_id":"5568","date_updated":"2026-04-08T14:20:15Z","abstract":[{"lang":"eng","text":"Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)"}],"has_accepted_license":"1","month":"08"},{"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"author":[{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek"}],"related_material":{"record":[{"id":"1591","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No","year":"2017","abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"_id":"938","date_updated":"2026-04-08T14:20:45Z","date_published":"2017-06-02T00:00:00Z","page":"117","citation":{"ieee":"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>","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","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>.","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.","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>"},"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"date_created":"2018-12-11T11:49:18Z","oa_version":"Published Version","type":"dissertation","status":"public","day":"02","publication_identifier":{"issn":["2663-337X"]},"file":[{"relation":"source_file","date_created":"2019-04-05T09:03:20Z","file_id":"6215","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"193425764d9aaaed3ac57062a867b315","creator":"dernst","date_updated":"2020-07-14T12:48:15Z","access_level":"closed","file_name":"2017_Adamowski-Thesis_Source.docx","file_size":46903863},{"relation":"main_file","date_created":"2019-04-05T09:03:19Z","file_id":"6216","checksum":"df5ab01be81f821e1b958596a1ec8d21","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","creator":"dernst","file_name":"2017_Adamowski-Thesis.pdf","access_level":"open_access","file_size":8698888}],"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ddc":["581","583","580"],"pubrep_id":"842","file_date_updated":"2020-07-14T12:48:15Z","doi":"10.15479/AT:ISTA:th_842","month":"06","publist_id":"6483","OA_place":"publisher","corr_author":"1"},{"article_processing_charge":"No","year":"2017","author":[{"first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin"}],"related_material":{"record":[{"status":"public","id":"666","relation":"part_of_dissertation"},{"id":"2001","status":"public","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_created":"2018-12-11T11:48:40Z","type":"dissertation","oa":1,"abstract":[{"lang":"eng","text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. "}],"_id":"818","date_updated":"2026-04-08T14:21:57Z","date_published":"2017-09-27T00:00:00Z","page":"113","department":[{"_id":"ToBo"}],"citation":{"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>","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>.","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.","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.","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>","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."},"language":[{"iso":"eng"}],"has_accepted_license":"1","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. ","supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X"}],"ddc":["571","579"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"degree_awarded":"PhD","publication_status":"published","publisher":"Institute of Science and Technology Austria","status":"public","day":"27","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_updated":"2020-07-14T12:48:09Z","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"da3993c5f90f59a8e8623cc31ad501dd","file_size":6331071,"access_level":"closed","file_name":"Thesis_KarinMitosch.docx","date_created":"2019-04-05T08:48:51Z","relation":"source_file","file_id":"6210"},{"file_size":9289852,"access_level":"open_access","file_name":"Thesis_KarinMitosch.pdf","date_updated":"2020-07-14T12:48:09Z","creator":"dernst","content_type":"application/pdf","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_id":"6211","relation":"main_file","date_created":"2019-04-05T08:48:51Z"}],"publist_id":"6831","corr_author":"1","OA_place":"publisher","month":"09","pubrep_id":"862","file_date_updated":"2020-07-14T12:48:09Z","doi":"10.15479/AT:ISTA:th_862"},{"quality_controlled":"1","ddc":["576","610"],"external_id":{"isi":["000402747300005"]},"publication":"Cell Systems","volume":4,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publisher":"Cell Press","publication_status":"published","day":"26","status":"public","file":[{"file_id":"5041","relation":"main_file","date_created":"2018-12-12T10:13:54Z","access_level":"open_access","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","file_size":2438660,"content_type":"application/pdf","checksum":"04ff20011c3d9a601c514aa999a5fe1a","creator":"system","date_updated":"2020-07-14T12:47:35Z"}],"publication_identifier":{"issn":["2405-4712"]},"publist_id":"7061","corr_author":"1","ec_funded":1,"month":"04","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.cels.2017.03.001","pubrep_id":"901","file_date_updated":"2020-07-14T12:47:35Z","project":[{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"year":"2017","article_processing_charge":"Yes (in subscription journal)","intvolume":"         4","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch"},{"first_name":"Georg","last_name":"Rieckh","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_created":"2018-12-11T11:47:48Z","oa_version":"Published Version","type":"journal_article","issue":"4","oa":1,"isi":1,"page":"393 - 403","date_published":"2017-04-26T00:00:00Z","citation":{"apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017."},"department":[{"_id":"ToBo"},{"_id":"GaTk"}],"_id":"666","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"date_updated":"2026-04-08T14:21:56Z","has_accepted_license":"1","language":[{"iso":"eng"}]},{"date_published":"2017-08-09T00:00:00Z","department":[{"_id":"KrCh"}],"page":"418","citation":{"ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>","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>.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","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>","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017."},"date_updated":"2026-04-08T14:22:17Z","_id":"821","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2018-12-11T11:48:41Z","type":"dissertation","oa":1,"alternative_title":["ISTA Thesis"],"title":"Algorithmic advances in program analysis and their applications","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2017","article_processing_charge":"No","author":[{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1602","status":"public"},{"relation":"part_of_dissertation","id":"1604","status":"public"},{"status":"public","id":"1437","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1071"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"status":"public","id":"1714","relation":"part_of_dissertation"}]},"month":"08","license":"https://creativecommons.org/licenses/by-nd/4.0/","doi":"10.15479/AT:ISTA:th_854","file_date_updated":"2020-07-14T12:48:10Z","pubrep_id":"854","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publist_id":"6828","OA_place":"publisher","corr_author":"1","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","publication_status":"published","degree_awarded":"PhD","day":"09","status":"public","file":[{"file_id":"4900","date_created":"2018-12-12T10:11:44Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","file_size":4103115,"checksum":"3a3ec003f6ee73f41f82a544d63dfc77","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:48:10Z"},{"file_size":14744374,"access_level":"closed","file_name":"2017_thesis_Pavlogiannis.zip","date_updated":"2020-07-14T12:48:10Z","creator":"dernst","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","content_type":"application/zip","file_id":"6201","date_created":"2019-04-05T07:59:31Z","relation":"source_file"}],"publication_identifier":{"issn":["2663-337X"]},"ddc":["000"],"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.","supervisor":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}]},{"day":"02","status":"public","file":[{"creator":"system","date_updated":"2020-07-14T12:44:34Z","content_type":"application/pdf","checksum":"1406a681cb737508234fde34766be2c2","file_size":1028586,"file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:26Z","file_id":"4880"}],"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_status":"published","ddc":["004","005"],"supervisor":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"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. ","doi":"10.15479/AT:ISTA:TH_730","pubrep_id":"730","file_date_updated":"2020-07-14T12:44:34Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"month":"01","ec_funded":1,"publist_id":"6203","OA_place":"publisher","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Statistical and logical methods for property checking","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2063"},{"status":"public","id":"1093","relation":"part_of_dissertation"},{"status":"public","id":"1391","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1234","status":"public"},{"id":"1230","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1501"},{"relation":"part_of_dissertation","status":"public","id":"1502"},{"relation":"part_of_dissertation","id":"2167","status":"public"}]},"year":"2017","article_processing_charge":"No","department":[{"_id":"ToHe"}],"citation":{"ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">10.15479/AT:ISTA:TH_730</a>","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","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>.","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>.","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>"},"page":"163","date_published":"2017-01-02T00:00:00Z","abstract":[{"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.","lang":"eng"}],"_id":"1155","date_updated":"2026-04-15T10:02:13Z","has_accepted_license":"1","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_created":"2018-12-11T11:50:27Z","type":"dissertation"},{"citation":{"short":"R. Remez, N. Shapira, C. Roques-Carmes, R. Tirole, Y. Yang, Y. Lereah, M. Soljačić, I. Kaminer, A. Arie, Physical Review A 96 (2017).","mla":"Remez, Roei, et al. “Spectral and Spatial Shaping of Smith-Purcell Radiation.” <i>Physical Review A</i>, vol. 96, no. 6, 061801, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physreva.96.061801\">10.1103/physreva.96.061801</a>.","apa":"Remez, R., Shapira, N., Roques-Carmes, C., Tirole, R., Yang, Y., Lereah, Y., … Arie, A. (2017). Spectral and spatial shaping of Smith-Purcell radiation. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.96.061801\">https://doi.org/10.1103/physreva.96.061801</a>","ista":"Remez R, Shapira N, Roques-Carmes C, Tirole R, Yang Y, Lereah Y, Soljačić M, Kaminer I, Arie A. 2017. Spectral and spatial shaping of Smith-Purcell radiation. Physical Review A. 96(6), 061801.","chicago":"Remez, Roei, Niv Shapira, Charles Roques-Carmes, Romain Tirole, Yi Yang, Yossi Lereah, Marin Soljačić, Ido Kaminer, and Ady Arie. “Spectral and Spatial Shaping of Smith-Purcell Radiation.” <i>Physical Review A</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physreva.96.061801\">https://doi.org/10.1103/physreva.96.061801</a>.","ieee":"R. Remez <i>et al.</i>, “Spectral and spatial shaping of Smith-Purcell radiation,” <i>Physical Review A</i>, vol. 96, no. 6. American Physical Society, 2017.","ama":"Remez R, Shapira N, Roques-Carmes C, et al. Spectral and spatial shaping of Smith-Purcell radiation. <i>Physical Review A</i>. 2017;96(6). doi:<a href=\"https://doi.org/10.1103/physreva.96.061801\">10.1103/physreva.96.061801</a>"},"date_published":"2017-12-06T00:00:00Z","_id":"21558","date_updated":"2026-04-15T11:46:22Z","abstract":[{"lang":"eng","text":"The Smith-Purcell effect, observed when an electron beam passes in the vicinity of a periodic structure, is a promising platform for the generation of electromagnetic radiation in previously unreachable spectral ranges. However, most of the studies of this radiation were performed on simple periodic gratings, whose radiation spectrum exhibits a single peak and its higher harmonics predicted by a well-established dispersion relation. Here, we propose a method to shape the spatial and spectral far-field distribution of the radiation using complex periodic and aperiodic gratings. We show, theoretically and experimentally, that engineering multiple peak spectra with controlled widths located at desired wavelengths is achievable using Smith-Purcell radiation. Our method opens the way to free-electron-driven sources with tailored angular and spectral responses, and gives rise to focusing functionality for spectral ranges where lenses are unavailable or inefficient."}],"language":[{"iso":"eng"}],"date_created":"2026-03-30T12:22:47Z","oa_version":"Preprint","type":"journal_article","article_number":"061801","issue":"6","oa":1,"title":"Spectral and spatial shaping of Smith-Purcell radiation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","year":"2017","article_processing_charge":"No","extern":"1","author":[{"first_name":"Roei","last_name":"Remez","full_name":"Remez, Roei"},{"full_name":"Shapira, Niv","first_name":"Niv","last_name":"Shapira"},{"last_name":"Roques-Carmes","first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles"},{"last_name":"Tirole","first_name":"Romain","full_name":"Tirole, Romain"},{"full_name":"Yang, Yi","last_name":"Yang","first_name":"Yi"},{"first_name":"Yossi","last_name":"Lereah","full_name":"Lereah, Yossi"},{"last_name":"Soljačić","first_name":"Marin","full_name":"Soljačić, Marin"},{"full_name":"Kaminer, Ido","first_name":"Ido","last_name":"Kaminer"},{"full_name":"Arie, Ady","last_name":"Arie","first_name":"Ady"}],"intvolume":"        96","article_type":"original","month":"12","doi":"10.1103/physreva.96.061801","OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1710.03719"}],"publication":"Physical Review A","volume":96,"publisher":"American Physical Society","publication_status":"published","day":"06","status":"public","arxiv":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"quality_controlled":"1","external_id":{"arxiv":["1710.03719"]},"ddc":["530"]},{"date_published":"2017-05-01T00:00:00Z","page":"43-58","citation":{"ieee":"M. Khorasaninejad <i>et al.</i>, “Visible wavelength planar metalenses based on titanium dioxide,” <i>IEEE Journal of Selected Topics in Quantum Electronics</i>, vol. 23, no. 3. Institute of Electrical and Electronics Engineers, pp. 43–58, 2017.","ama":"Khorasaninejad M, Chen WT, Zhu AY, et al. Visible wavelength planar metalenses based on titanium dioxide. <i>IEEE Journal of Selected Topics in Quantum Electronics</i>. 2017;23(3):43-58. doi:<a href=\"https://doi.org/10.1109/jstqe.2016.2616447\">10.1109/jstqe.2016.2616447</a>","ista":"Khorasaninejad M, Chen WT, Zhu AY, Oh J, Devlin RC, Roques-Carmes C, Mishra I, Capasso F. 2017. Visible wavelength planar metalenses based on titanium dioxide. IEEE Journal of Selected Topics in Quantum Electronics. 23(3), 43–58.","chicago":"Khorasaninejad, Mohammadreza, Wei Ting Chen, Alexander Y. Zhu, Jaewon Oh, Robert C. Devlin, Charles Roques-Carmes, Ishan Mishra, and Federico Capasso. “Visible Wavelength Planar Metalenses Based on Titanium Dioxide.” <i>IEEE Journal of Selected Topics in Quantum Electronics</i>. Institute of Electrical and Electronics Engineers, 2017. <a href=\"https://doi.org/10.1109/jstqe.2016.2616447\">https://doi.org/10.1109/jstqe.2016.2616447</a>.","mla":"Khorasaninejad, Mohammadreza, et al. “Visible Wavelength Planar Metalenses Based on Titanium Dioxide.” <i>IEEE Journal of Selected Topics in Quantum Electronics</i>, vol. 23, no. 3, Institute of Electrical and Electronics Engineers, 2017, pp. 43–58, doi:<a href=\"https://doi.org/10.1109/jstqe.2016.2616447\">10.1109/jstqe.2016.2616447</a>.","short":"M. Khorasaninejad, W.T. Chen, A.Y. Zhu, J. Oh, R.C. Devlin, C. Roques-Carmes, I. Mishra, F. Capasso, IEEE Journal of Selected Topics in Quantum Electronics 23 (2017) 43–58.","apa":"Khorasaninejad, M., Chen, W. T., Zhu, A. Y., Oh, J., Devlin, R. C., Roques-Carmes, C., … Capasso, F. (2017). Visible wavelength planar metalenses based on titanium dioxide. <i>IEEE Journal of Selected Topics in Quantum Electronics</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/jstqe.2016.2616447\">https://doi.org/10.1109/jstqe.2016.2616447</a>"},"date_updated":"2026-04-15T12:14:59Z","_id":"21569","abstract":[{"text":"We present recent advances in metasurface-based photonics, which enables the realization of high performance planar lenses (metalenses) in the visible spectrum. They are enabled by a technique based on atomic layer deposition of titanium dioxide allowing for the fabrication of nanostructures with high fidelity. First, we demonstrate highly efficient metalenses with numerical aperture NA = 0.8 using the Pancharatnam-Berry phase approach. These metalenses can focus light into a diffraction-limited spot. They have efficiencies as high as 86% and provide high imaging resolution. Furthermore, by judicious design of the phase-shifting elements, we achieve a multispectral chiral metalens realized with a single metasurface layer. This chiral metalens can resolve both the chiral and spectral information of an object without the requirement of any additional optical components. Finally, we discuss the experimental realization of polarization-insensitive metalenses with NAs as high as 0.85. They are able to focus incident light to a spot as small as ~0.64λ with efficiencies up to 60%. Due to its straightforward and CMOS-compatible fabrication, this platform is promising for a wide range of applications ranging from camera modules, displays, laser-based imaging, microscopy, and spectroscopy to laser fabrication and lithography.","lang":"eng"}],"language":[{"iso":"eng"}],"issue":"3","oa_version":"None","date_created":"2026-03-30T12:22:47Z","type":"journal_article","title":"Visible wavelength planar metalenses based on titanium dioxide","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","author":[{"full_name":"Khorasaninejad, Mohammadreza","last_name":"Khorasaninejad","first_name":"Mohammadreza"},{"full_name":"Chen, Wei Ting","last_name":"Chen","first_name":"Wei Ting"},{"full_name":"Zhu, Alexander Y.","last_name":"Zhu","first_name":"Alexander Y."},{"full_name":"Oh, Jaewon","first_name":"Jaewon","last_name":"Oh"},{"full_name":"Devlin, Robert C.","first_name":"Robert C.","last_name":"Devlin"},{"full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","first_name":"Charles"},{"full_name":"Mishra, Ishan","first_name":"Ishan","last_name":"Mishra"},{"full_name":"Capasso, Federico","last_name":"Capasso","first_name":"Federico"}],"intvolume":"        23","article_type":"original","year":"2017","article_processing_charge":"No","extern":"1","doi":"10.1109/jstqe.2016.2616447","OA_type":"closed access","month":"05","day":"01","status":"public","publication_identifier":{"issn":["1077-260X"],"eissn":["1558-4542"]},"publication":"IEEE Journal of Selected Topics in Quantum Electronics","volume":23,"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","quality_controlled":"1"},{"year":"2017","article_processing_charge":"No","intvolume":"      2184","author":[{"first_name":"Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"full_name":"Romon, Pascal","first_name":"Pascal","last_name":"Romon"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Entropic Ricci curvature for discrete spaces","scopus_import":"1","oa_version":"None","date_created":"2018-12-11T11:47:42Z","type":"book_chapter","citation":{"short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>.","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman &#38; P. Romon (Eds.), <i>Modern Approaches to Discrete Curvature</i> (Vol. 2184, pp. 159–174). Springer. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. <i>Modern Approaches to Discrete Curvature</i>. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in <i>Modern Approaches to Discrete Curvature</i>, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>."},"page":"159 - 174","department":[{"_id":"JaMa"}],"date_published":"2017-10-05T00:00:00Z","abstract":[{"lang":"eng","text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani."}],"_id":"649","date_updated":"2026-04-16T08:59:01Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Modern Approaches to Discrete Curvature","volume":2184,"series_title":"Lecture Notes in Mathematics","publisher":"Springer","publication_status":"published","day":"05","status":"public","publication_identifier":{"isbn":["9783319580012"],"eisbn":["9783319580029"]},"publist_id":"7123","corr_author":"1","month":"10","doi":"10.1007/978-3-319-58002-9_5"},{"month":"06","file_date_updated":"2020-07-14T12:44:44Z","pubrep_id":"658","doi":"10.1007/s00453-016-0212-1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"}],"publist_id":"5931","ec_funded":1,"volume":78,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Algorithmica","publication_status":"published","publisher":"Springer","status":"public","day":"01","publication_identifier":{"issn":["0178-4617"]},"file":[{"access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","file_size":710206,"content_type":"application/pdf","checksum":"7873f665a0c598ac747c908f34cb14b9","date_updated":"2020-07-14T12:44:44Z","creator":"system","file_id":"4805","date_created":"2018-12-12T10:10:19Z","relation":"main_file"}],"quality_controlled":"1","external_id":{"isi":["000400379500013"]},"ddc":["576"],"_id":"1336","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"date_updated":"2026-04-16T09:55:33Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"page":"681 - 713","date_published":"2017-06-01T00:00:00Z","citation":{"apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713."},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","date_created":"2018-12-11T11:51:27Z","type":"journal_article","issue":"2","isi":1,"oa":1,"title":"Towards a runtime comparison of natural and artificial evolution","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","article_processing_charge":"No","year":"2017","intvolume":"        78","author":[{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}]}]