[{"arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"type":"conference","month":"03","intvolume":"     10205","page":"443-460","citation":{"short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>"},"quality_controlled":"1","alternative_title":["LNCS"],"publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","publisher":"Springer","title":"Index appearance record for transforming Rabin automata into parity automata","article_processing_charge":"No","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Uppsala, Sweden","start_date":"2017-04-22","end_date":"2017-04-29"},"_id":"13160","date_updated":"2023-06-21T13:29:46Z","year":"2017","acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","publication_identifier":{"isbn":["9783662545768"],"eisbn":["9783662545775"],"issn":["0302-9743"],"eissn":["1611-3349"]},"oa":1,"author":[{"first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"last_name":"Waldmann","first_name":"Clara","full_name":"Waldmann, Clara"},{"last_name":"Weininger","full_name":"Weininger, Maximilian","first_name":"Maximilian"}],"status":"public","oa_version":"Preprint","volume":10205,"date_created":"2023-06-21T13:21:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-54577-5_26","external_id":{"arxiv":["1701.05738"]},"date_published":"2017-03-31T00:00:00Z","day":"31"},{"year":"2017","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","project":[{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","title":"The lac operon in the wild","_id":"820","date_updated":"2023-09-07T12:01:21Z","day":"25","date_published":"2017-08-25T00:00:00Z","oa_version":"Published Version","author":[{"last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne","first_name":"Fabienne"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.15479/AT:ISTA:th_857","date_created":"2018-12-11T11:48:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pubrep_id":"857","month":"08","ec_funded":1,"page":"87","degree_awarded":"PhD","type":"dissertation","ddc":["576","577","579"],"abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"publist_id":"6829","department":[{"_id":"JoBo"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","file_size":3417773,"date_created":"2018-12-12T10:17:00Z","relation":"main_file","file_id":"5252","access_level":"open_access","creator":"system","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","content_type":"application/pdf"},{"access_level":"closed","creator":"dernst","content_type":"application/x-tex","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_id":"6212","relation":"source_file","date_updated":"2020-07-14T12:48:10Z","file_name":"2017_thesis_Jesse_source.tex","file_size":215899,"date_created":"2019-04-05T08:51:59Z"}],"file_date_updated":"2020-07-14T12:48:10Z","citation":{"mla":"Jesse, Fabienne. <i>The Lac Operon in the Wild</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>.","apa":"Jesse, F. (2017). <i>The lac operon in the wild</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>","ama":"Jesse F. The lac operon in the wild. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>"},"alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by/4.0/","supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"publist_id":"6828","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"file":[{"relation":"main_file","file_size":4103115,"date_created":"2018-12-12T10:11:44Z","date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"4900"},{"access_level":"closed","creator":"dernst","content_type":"application/zip","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","file_id":"6201","relation":"source_file","date_updated":"2020-07-14T12:48:10Z","file_name":"2017_thesis_Pavlogiannis.zip","file_size":14744374,"date_created":"2019-04-05T07:59:31Z"}],"file_date_updated":"2020-07-14T12:48:10Z","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"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>","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>.","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>","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.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria."},"publication_status":"published","supervisor":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","month":"08","pubrep_id":"854","degree_awarded":"PhD","page":"418","ec_funded":1,"ddc":["000"],"type":"dissertation","date_published":"2017-08-09T00:00:00Z","day":"09","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"},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:48:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/AT:ISTA:th_854","has_accepted_license":"1","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"year":"2017","publication_identifier":{"issn":["2663-337X"]},"oa":1,"article_processing_charge":"No","title":"Algorithmic advances in program analysis and their applications","related_material":{"record":[{"status":"public","id":"1071","relation":"part_of_dissertation"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1602","relation":"part_of_dissertation"},{"status":"public","id":"1604","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"status":"public","id":"1714","relation":"part_of_dissertation"}]},"date_updated":"2023-09-07T12:01:59Z","_id":"821"},{"quality_controlled":"1","citation":{"ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” <i>PNAS</i>, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. 2017;114(40):10666-10671. doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., &#38; Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>"},"publication_status":"published","abstract":[{"text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. ","lang":"eng"}],"publist_id":"6827","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"publisher":"National Academy of Sciences","publication":"PNAS","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}],"type":"journal_article","intvolume":"       114","month":"10","isi":1,"page":"10666 - 10671","ec_funded":1,"issue":"40","oa_version":"Submitted Version","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","full_name":"De Vos, Marjon","first_name":"Marjon"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762"},{"last_name":"Mcnally","full_name":"Mcnally, Alan","first_name":"Alan"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"}],"status":"public","pmid":1,"doi":"10.1073/pnas.1713372114","date_created":"2018-12-11T11:48:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":114,"external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"day":"03","date_published":"2017-10-03T00:00:00Z","article_processing_charge":"No","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","date_updated":"2023-09-26T16:18:48Z","_id":"822","year":"2017","project":[{"call_identifier":"FP7","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","name":"Optimality principles in responses to antibiotics"},{"grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_identifier":{"issn":["00278424"]}},{"citation":{"ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2017. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>.","apa":"Colabrese, S., De Martino, D., Leuzzi, L., &#38; Marinari, E. (2017). Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9. IOPscience, 2017.","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>."},"quality_controlled":"1","publication_status":"published","publist_id":"6826","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region."}],"publication":" Journal of Statistical Mechanics: Theory and Experiment","scopus_import":"1","publisher":"IOPscience","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"type":"journal_article","month":"09","isi":1,"article_number":"093404","intvolume":"      2017","issue":"9","ec_funded":1,"status":"public","author":[{"last_name":"Colabrese","full_name":"Colabrese, Simona","first_name":"Simona"},{"first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"},{"first_name":"Luca","full_name":"Leuzzi, Luca","last_name":"Leuzzi"},{"last_name":"Marinari","first_name":"Enzo","full_name":"Marinari, Enzo"}],"oa_version":"Submitted Version","volume":2017,"date_created":"2018-12-11T11:48:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1088/1742-5468/aa85c3","external_id":{"isi":["000411842900001"]},"date_published":"2017-09-26T00:00:00Z","day":"26","article_processing_charge":"No","title":"Phase transitions in integer linear problems","_id":"823","date_updated":"2023-09-26T16:18:12Z","year":"2017","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_identifier":{"issn":["17425468"]},"oa":1},{"title":"Heteroclinic path to spatially localized chaos in pipe flow","article_processing_charge":"No","_id":"824","date_updated":"2023-09-26T16:17:43Z","year":"2017","oa":1,"publication_identifier":{"issn":["00221120"]},"oa_version":"Submitted Version","status":"public","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn"}],"doi":"10.1017/jfm.2017.516","volume":827,"date_created":"2018-12-11T11:48:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000408326300001"]},"day":"18","date_published":"2017-08-18T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1703.10484","open_access":"1"}],"type":"journal_article","article_number":"R1","intvolume":"       827","month":"08","isi":1,"citation":{"ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;827. doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>","apa":"Budanur, N. B., &#38; Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>.","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 827. Cambridge University Press, 2017.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 827, R1, Cambridge University Press, 2017, doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>."},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff."}],"department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"publist_id":"6824","publisher":"Cambridge University Press","publication":"Journal of Fluid Mechanics","scopus_import":"1"},{"author":[{"last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","first_name":"Barbara"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:42Z","volume":70,"doi":"10.31263/voebm.v70i2.1678","date_published":"2017-08-01T00:00:00Z","day":"01","title":"Metadata for research data in practice","date_updated":"2021-01-12T08:17:44Z","_id":"825","has_accepted_license":"1","year":"2017","publication_identifier":{"issn":["10222588"]},"oa":1,"citation":{"ama":"Petritsch B. Metadata for research data in practice. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. 2017;70(2):200-207. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>.","apa":"Petritsch, B. (2017). Metadata for research data in practice. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>","ieee":"B. Petritsch, “Metadata for research data in practice,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare. 70(2), 200–207.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare 70 (2017) 200–207."},"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"6823","department":[{"_id":"E-Lib"}],"abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"scopus_import":1,"file":[{"checksum":"7c4544d07efa2c2add8612b489abb4e2","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5850","relation":"main_file","file_size":7843975,"date_created":"2019-01-18T13:32:17Z","date_updated":"2020-07-14T12:48:11Z","file_name":"2017_VOEB_Petritsch.pdf"}],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","file_date_updated":"2020-07-14T12:48:11Z","publisher":"VÖB","ddc":["020"],"type":"journal_article","month":"08","intvolume":"        70","issue":"2","page":"200 - 207"},{"editor":[{"last_name":"Felsberg","first_name":"Michael","full_name":"Felsberg, Michael"},{"first_name":"Anders","full_name":"Heyden, Anders","last_name":"Heyden"},{"last_name":"Krüger","first_name":"Norbert","full_name":"Krüger, Norbert"}],"abstract":[{"lang":"eng","text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams."}],"publist_id":"6815","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publisher":"Springer","scopus_import":"1","alternative_title":["LNCS"],"quality_controlled":"1","citation":{"apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>.","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409."},"publication_status":"published","intvolume":"     10424","isi":1,"month":"07","page":"397 - 409","main_file_link":[{"url":"https://arxiv.org/abs/1705.02045","open_access":"1"}],"type":"conference","external_id":{"isi":["000432085900032"]},"day":"28","date_published":"2017-07-28T00:00:00Z","oa_version":"Submitted Version","status":"public","author":[{"last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa"},{"last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","full_name":"Wagner, Hubert"}],"doi":"10.1007/978-3-319-64689-3_32","date_created":"2018-12-11T11:48:45Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10424,"year":"2017","oa":1,"publication_identifier":{"issn":["03029743"]},"article_processing_charge":"No","title":"Streaming algorithm for Euler characteristic curves of multidimensional images","date_updated":"2023-09-26T16:10:03Z","_id":"833","conference":{"name":"CAIP: Computer Analysis of Images and Patterns","location":"Ystad, Sweden","start_date":"2017-08-22","end_date":"2017-08-24"}},{"article_processing_charge":"No","title":"Thouless energy and multifractality across the many-body localization transition","date_updated":"2023-09-26T15:51:54Z","_id":"834","acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","year":"2017","oa":1,"publication_identifier":{"issn":["24699950"]},"oa_version":"Submitted Version","author":[{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"},{"last_name":"Zlatko","full_name":"Zlatko, Papic","first_name":"Papic"},{"first_name":"Dmitry","full_name":"Abanin, Dmitry","last_name":"Abanin"}],"status":"public","doi":"10.1103/PhysRevB.96.104201","date_created":"2018-12-11T11:48:45Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":96,"external_id":{"isi":["000409429300004"]},"day":"06","date_published":"2017-09-06T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1610.02389","open_access":"1"}],"type":"journal_article","intvolume":"        96","article_number":"104201","isi":1,"month":"09","issue":"10","quality_controlled":"1","citation":{"ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201.","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10. American Physical Society, 2017.","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>.","short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017)."},"publication_status":"published","abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"publist_id":"6814","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication":"Physical Review B - Condensed Matter and Materials Physics","scopus_import":"1"},{"publication_status":"published","quality_controlled":"1","alternative_title":["PROMS"],"citation":{"short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” <i>Special Sessions in Applications of Computer Algebra</i>, vol. 198, Springer, 2017, pp. 119–36, doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in <i>Special Sessions in Applications of Computer Algebra</i>, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","apa":"Ethier, M., Jablonski, G., &#38; Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In <i>Special Sessions in Applications of Computer Algebra</i> (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In <i>Special Sessions in Applications of Computer Algebra</i>, 198:119–36. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>.","ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: <i>Special Sessions in Applications of Computer Algebra</i>. Vol 198. Springer; 2017:119-136. doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>"},"publisher":"Springer","scopus_import":"1","publication":"Special Sessions in Applications of Computer Algebra","abstract":[{"lang":"eng","text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces."}],"language":[{"iso":"eng"}],"publist_id":"6812","department":[{"_id":"HeEd"}],"type":"conference","page":"119 - 136","ec_funded":1,"intvolume":"       198","isi":1,"month":"07","doi":"10.1007/978-3-319-56932-1_8","date_created":"2018-12-11T11:48:46Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":198,"oa_version":"None","author":[{"first_name":"Marc","full_name":"Ethier, Marc","last_name":"Ethier"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","first_name":"Grzegorz","full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866"},{"first_name":"Marian","full_name":"Mrozek, Marian","last_name":"Mrozek"}],"status":"public","day":"27","date_published":"2017-07-27T00:00:00Z","external_id":{"isi":["000434088200008"]},"date_updated":"2023-09-26T15:50:52Z","_id":"836","conference":{"name":"ACA: Applications of Computer Algebra","location":"Kalamata, Greece","start_date":"2015-07-20","end_date":"2015-07-23"},"title":"Finding eigenvalues of self-maps with the Kronecker canonical form","article_processing_charge":"No","publication_identifier":{"isbn":["978-331956930-7"]},"project":[{"grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"year":"2017"},{"pubrep_id":"858","month":"08","page":"93","degree_awarded":"PhD","ddc":["571"],"type":"dissertation","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"publist_id":"6811","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2020-07-14T12:48:12Z","file_name":"2017_Xu_Haibing_Thesis_Source.docx","file_size":3589490,"date_created":"2019-04-05T08:59:51Z","relation":"source_file","file_id":"6213","access_level":"closed","creator":"dernst","checksum":"f11925fbbce31e495124b6bc4f10573c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"6214","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"ffb10749a537d615fab1ef0937ccb157","file_name":"2017_Xu_Thesis_IST.pdf","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","file_size":11668613,"relation":"main_file"}],"file_date_updated":"2020-07-14T12:48:12Z","alternative_title":["ISTA Thesis"],"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>.","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>","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>","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.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria."},"publication_status":"published","supervisor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"}],"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. ","year":"2017","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","date_updated":"2023-09-07T12:06:38Z","_id":"837","related_material":{"record":[{"status":"public","id":"5828","relation":"part_of_dissertation"}]},"day":"23","date_published":"2017-08-23T00:00:00Z","oa_version":"Published Version","author":[{"first_name":"Haibing","full_name":"Xu, Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.15479/AT:ISTA:th_858","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:46Z"},{"oa":1,"publication_identifier":{"issn":["2663-337X"]},"year":"2017","has_accepted_license":"1","_id":"838","date_updated":"2023-09-07T12:02:28Z","related_material":{"record":[{"id":"2082","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6196","status":"public"}]},"title":"(The exact security of) Message authentication codes","article_processing_charge":"No","day":"26","date_published":"2017-06-26T00:00:00Z","doi":"10.15479/AT:ISTA:th_828","date_created":"2018-12-11T11:48:46Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","status":"public","author":[{"full_name":"Rybar, Michal","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar"}],"page":"86","degree_awarded":"PhD","pubrep_id":"828","month":"06","type":"dissertation","ddc":["000"],"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","date_updated":"2020-07-14T12:48:12Z","date_created":"2018-12-12T10:10:13Z","file_size":847400,"relation":"main_file","file_id":"4799","creator":"system","access_level":"open_access","checksum":"ff8639ec4bded6186f44c7bd3ee26804","content_type":"application/pdf"},{"file_size":26054879,"date_created":"2019-04-05T08:24:11Z","file_name":"2017_Thesis_Rybar_source.zip","date_updated":"2020-07-14T12:48:12Z","relation":"source_file","file_id":"6202","checksum":"3462101745ce8ad199c2d0f75dae4a7e","content_type":"application/zip","creator":"dernst","access_level":"closed"}],"file_date_updated":"2020-07-14T12:48:12Z","abstract":[{"text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ","lang":"eng"}],"department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"publist_id":"6810","publication_status":"published","citation":{"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>.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","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>.","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>","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>"},"alternative_title":["ISTA Thesis"]},{"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1362"},{"relation":"part_of_dissertation","status":"public","id":"1633"},{"relation":"popular_science","status":"public","id":"5568"}]},"date_updated":"2024-02-21T13:48:02Z","_id":"839","article_processing_charge":"No","title":"Brittle fracture simulation with boundary elements for computer graphics","publication_identifier":{"issn":["2663-337X"]},"oa":1,"has_accepted_license":"1","year":"2017","project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"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","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:47Z","doi":"10.15479/AT:ISTA:th_855","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"author":[{"first_name":"David","full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn"}],"status":"public","oa_version":"Published Version","date_published":"2017-08-14T00:00:00Z","day":"14","ddc":["004","005","006","531","621"],"type":"dissertation","degree_awarded":"PhD","page":"124","ec_funded":1,"month":"08","pubrep_id":"855","publication_status":"published","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","alternative_title":["ISTA Thesis"],"citation":{"ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","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>","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","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>."},"file":[{"creator":"system","access_level":"open_access","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","content_type":"application/pdf","file_id":"5100","relation":"main_file","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","date_updated":"2020-07-14T12:48:13Z","date_created":"2018-12-12T10:14:46Z","file_size":14596191},{"content_type":"application/zip","checksum":"421672f68d563b029869c5cf1713f919","access_level":"closed","creator":"dernst","file_id":"6207","relation":"source_file","file_size":15060566,"date_created":"2019-04-05T08:40:30Z","date_updated":"2020-07-14T12:48:13Z","file_name":"2017_thesis_Hahn_source.zip"}],"file_date_updated":"2020-07-14T12:48:13Z","publisher":"Institute of Science and Technology Austria","publist_id":"6809","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"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"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:44:32Z","doi":"10.1201/9781315119601","quality_controlled":"1","series_title":"Handbook of Discrete and Computational Geometry","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Koehl","full_name":"Koehl, Patrice","first_name":"Patrice"}],"status":"public","citation":{"chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735.","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735.","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735."},"oa_version":"None","date_published":"2017-11-09T00:00:00Z","scopus_import":"1","publication":"Handbook of Discrete and Computational Geometry, Third Edition","publisher":"Taylor & Francis","day":"09","department":[{"_id":"HeEd"}],"publist_id":"7970","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind."}],"editor":[{"last_name":"Toth","full_name":"Toth, Csaba","first_name":"Csaba"},{"last_name":"O'Rourke","first_name":"Joseph","full_name":"O'Rourke, Joseph"},{"full_name":"Goodman, Jacob","first_name":"Jacob","last_name":"Goodman"}],"date_updated":"2023-10-16T11:15:22Z","type":"book_chapter","_id":"84","title":"Computational topology for structural molecular biology","article_processing_charge":"No","publication_identifier":{"eisbn":["9781498711425"]},"page":"1709 - 1735","month":"11","year":"2017"},{"date_updated":"2023-09-26T15:50:22Z","_id":"840","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"status":"public","relation":"dissertation_contains","id":"69"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"article_processing_charge":"No","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","oa":1,"publication_identifier":{"issn":["15306984"]},"year":"2017","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","grant_number":"335497"}],"has_accepted_license":"1","doi":"10.1021/acs.nanolett.7b02627","date_created":"2018-12-11T11:48:47Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":17,"oa_version":"Published Version","author":[{"first_name":"Lada","full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukusic"},{"last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip"},{"last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","day":"10","date_published":"2017-08-10T00:00:00Z","external_id":{"isi":["000411043500078"]},"ddc":["539"],"type":"journal_article","page":"5706 - 5710","acknowledged_ssus":[{"_id":"M-Shop"}],"ec_funded":1,"issue":"9","intvolume":"        17","pubrep_id":"865","isi":1,"month":"08","publication_status":"published","quality_controlled":"1","citation":{"chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., &#38; Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. 2017;17(9):5706-5710. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>.","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” <i>Nano Letters</i>, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710."},"publisher":"American Chemical Society","scopus_import":"1","publication":"Nano Letters","file_date_updated":"2020-07-14T12:48:13Z","file":[{"content_type":"application/pdf","checksum":"761371a0129b2aa442424b9561450ece","access_level":"open_access","creator":"system","file_id":"4951","relation":"main_file","file_size":2449546,"date_created":"2018-12-12T10:12:33Z","date_updated":"2020-07-14T12:48:13Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf"}],"abstract":[{"lang":"eng","text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements."}],"department":[{"_id":"GeKa"}],"language":[{"iso":"eng"}],"publist_id":"6808"},{"title":"On the lengths of curves passing through boundary points of a planar convex shape","article_processing_charge":"No","_id":"909","date_updated":"2023-10-17T11:24:57Z","year":"2017","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["00029890"]},"oa":1,"author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vladislav","full_name":"Vysotsky, Vladislav","last_name":"Vysotsky"}],"status":"public","oa_version":"Submitted Version","volume":124,"date_created":"2018-12-11T11:49:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4169/amer.math.monthly.124.7.588","external_id":{"arxiv":["1605.07997"],"isi":["000413947300002"]},"date_published":"2017-01-01T00:00:00Z","day":"01","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1605.07997","open_access":"1"}],"type":"journal_article","month":"01","isi":1,"intvolume":"       124","issue":"7","ec_funded":1,"page":"588 - 596","citation":{"ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” <i>The American Mathematical Monthly</i>, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. 2017;124(7):588-596. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>","apa":"Akopyan, A., &#38; Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>. Mathematical Association of America, 2017. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>."},"quality_controlled":"1","publication_status":"published","article_type":"original","language":[{"iso":"eng"}],"publist_id":"6534","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &amp;#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape."}],"publication":"The American Mathematical Monthly","scopus_import":"1","publisher":"Mathematical Association of America"},{"citation":{"chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>.","apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668."},"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"6533","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","file_date_updated":"2020-07-14T12:48:15Z","file":[{"file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","content_type":"application/pdf","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:17:12Z","file_size":494268,"file_name":"IST-2018-974-v1+1_manuscript.pdf","date_updated":"2020-07-14T12:48:15Z","relation":"main_file"}],"scopus_import":"1","publication":"Genetics","type":"journal_article","ddc":["576"],"pubrep_id":"974","intvolume":"       207","isi":1,"month":"10","ec_funded":1,"page":"653 - 668","issue":"2","oa_version":"Submitted Version","author":[{"first_name":"Sebastian","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"status":"public","doi":"10.1534/genetics.117.300129","volume":207,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:09Z","external_id":{"isi":["000412232600019"]},"day":"01","date_published":"2017-10-01T00:00:00Z","article_processing_charge":"No","title":"When does frequency-independent selection maintain genetic variation?","_id":"910","date_updated":"2023-09-26T15:49:15Z","year":"2017","project":[{"call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"has_accepted_license":"1","oa":1},{"date_updated":"2023-10-16T10:04:02Z","_id":"911","conference":{"start_date":"2017-09-04","end_date":"2017-09-07","location":"London, United Kingdom","name":"BMVC: British Machine Vision Conference"},"related_material":{"record":[{"status":"public","id":"8390","relation":"dissertation_contains"}]},"article_processing_charge":"No","title":"Probabilistic image colorization","oa":1,"publication_identifier":{"eisbn":["190172560X"]},"project":[{"grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"year":"2017","has_accepted_license":"1","doi":"10.5244/c.31.85","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:09Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","first_name":"Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"status":"public","day":"01","date_published":"2017-09-01T00:00:00Z","external_id":{"arxiv":["1705.04258"]},"ddc":["000"],"type":"conference","arxiv":1,"page":"85.1-85.12","ec_funded":1,"month":"09","publication_status":"published","quality_controlled":"1","citation":{"ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","mla":"Royer, Amélie, et al. <i>Probabilistic Image Colorization</i>. BMVA Press, 2017, p. 85.1-85.12, doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>.","apa":"Royer, A., Kolesnikov, A., &#38; Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>"},"publisher":"BMVA Press","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_id":"8224","relation":"main_file","date_updated":"2020-08-10T07:14:33Z","file_name":"2017_BMVC_Royer.pdf","file_size":1625363,"success":1,"date_created":"2020-08-10T07:14:33Z"}],"scopus_import":"1","file_date_updated":"2020-08-10T07:14:33Z","abstract":[{"text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"6532","department":[{"_id":"ChLa"}]},{"publication_identifier":{"issn":["00222488"]},"oa":1,"year":"2017","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}],"_id":"912","date_updated":"2024-02-28T13:07:56Z","article_processing_charge":"No","title":"A lower bound for the BCS functional with boundary conditions at infinity","date_published":"2017-08-01T00:00:00Z","day":"01","external_id":{"isi":["000409197200015"]},"volume":58,"date_created":"2018-12-11T11:49:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1063/1.4996580","status":"public","author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","full_name":"Deuchert, Andreas","first_name":"Andreas","orcid":"0000-0003-3146-6746"}],"oa_version":"Submitted Version","issue":"8","ec_funded":1,"month":"08","isi":1,"article_number":"081901","intvolume":"        58","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"scopus_import":"1","publication":" Journal of Mathematical Physics","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"publist_id":"6531","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"}],"publication_status":"published","citation":{"short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>.","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8. AIP Publishing, 2017.","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901.","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. 2017;58(8). doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>"},"quality_controlled":"1"},{"date_published":"2017-07-05T00:00:00Z","day":"05","external_id":{"isi":["000406670000025"]},"date_created":"2018-12-11T11:49:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":4,"doi":"10.1098/rsos.170547","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Giehr","full_name":"Giehr, Julia","first_name":"Julia"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V","first_name":"Anna V"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"}],"status":"public","oa_version":"Published Version","publication_identifier":{"issn":["20545703"]},"oa":1,"has_accepted_license":"1","year":"2017","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","related_material":{"record":[{"status":"public","id":"9853","relation":"research_data"}]},"date_updated":"2023-09-26T15:45:47Z","_id":"914","title":"Ant queens increase their reproductive efforts after pathogen infection","article_processing_charge":"No","publication":"Royal Society Open Science","file":[{"file_id":"4684","checksum":"351ae5e7a37e6e7d9295cd41146c4190","content_type":"application/pdf","creator":"system","access_level":"open_access","file_size":530412,"date_created":"2018-12-12T10:08:24Z","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","date_updated":"2020-07-14T12:48:15Z","relation":"main_file"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:15Z","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"publist_id":"6527","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect."}],"publication_status":"published","quality_controlled":"1","citation":{"chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>. Royal Society, The, 2017. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>.","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., &#38; Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. 2017;4(7). doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” <i>Royal Society Open Science</i>, vol. 4, no. 7. Royal Society, The, 2017."},"issue":"7","isi":1,"month":"07","pubrep_id":"849","intvolume":"         4","article_number":"170547","ddc":["576","592"],"type":"journal_article"}]