[{"has_accepted_license":"1","year":"2017","tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"date_updated":"2023-09-07T12:01:59Z","file":[{"checksum":"3a3ec003f6ee73f41f82a544d63dfc77","date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","relation":"main_file","file_id":"4900","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:11:44Z","file_size":4103115},{"date_created":"2019-04-05T07:59:31Z","file_size":14744374,"creator":"dernst","access_level":"closed","content_type":"application/zip","relation":"source_file","file_id":"6201","date_updated":"2020-07-14T12:48:10Z","file_name":"2017_thesis_Pavlogiannis.zip","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83"}],"article_processing_charge":"No","_id":"821","ec_funded":1,"publist_id":"6828","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:10Z","ddc":["000"],"publication_status":"published","page":"418","title":"Algorithmic advances in program analysis and their applications","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"department":[{"_id":"KrCh"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_created":"2018-12-11T11:48:41Z","citation":{"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.","chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854"},"oa_version":"Published Version","degree_awarded":"PhD","month":"08","pubrep_id":"854","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","doi":"10.15479/AT:ISTA:th_854","date_published":"2017-08-09T00:00:00Z","related_material":{"record":[{"id":"1071","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1437"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"status":"public","id":"1604","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1607","status":"public"},{"id":"1714","relation":"part_of_dissertation","status":"public"}]},"status":"public","oa":1,"day":"09"},{"oa_version":"Submitted Version","citation":{"ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1713372114.","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.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 2017;114(40):10666-10671. doi:10.1073/pnas.1713372114","mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114"},"date_created":"2018-12-11T11:48:41Z","publication":"PNAS","type":"journal_article","quality_controlled":"1","month":"10","status":"public","isi":1,"date_published":"2017-10-03T00:00:00Z","doi":"10.1073/pnas.1713372114","intvolume":" 114","oa":1,"external_id":{"pmid":["28923953"],"isi":["000412130500061"]},"day":"03","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"scopus_import":"1","issue":"40","year":"2017","volume":114,"abstract":[{"lang":"eng","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. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-26T16:18:48Z","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon","last_name":"De Vos"},{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"full_name":"Mcnally, Alan","last_name":"Mcnally","first_name":"Alan"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"}],"publication_identifier":{"issn":["00278424"]},"pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"_id":"822","publisher":"National Academy of Sciences","publist_id":"6827","department":[{"_id":"ToBo"}],"title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","page":"10666 - 10671","project":[{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22"}]},{"article_processing_charge":"No","date_updated":"2023-09-26T16:18:12Z","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"author":[{"first_name":"Simona","last_name":"Colabrese","full_name":"Colabrese, Simona"},{"orcid":"0000-0002-5214-4706","first_name":"Daniele","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"},{"last_name":"Leuzzi","full_name":"Leuzzi, Luca","first_name":"Luca"},{"first_name":"Enzo","full_name":"Marinari, Enzo","last_name":"Marinari"}],"publication_identifier":{"issn":["17425468"]},"issue":"9","scopus_import":"1","year":"2017","volume":2017,"department":[{"_id":"GaTk"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"title":"Phase transitions in integer linear problems","publication_status":"published","publisher":"IOPscience","publist_id":"6826","ec_funded":1,"_id":"823","quality_controlled":"1","month":"09","publication":" Journal of Statistical Mechanics: Theory and Experiment","oa_version":"Submitted Version","citation":{"ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017;2017(9). doi:10.1088/1742-5468/aa85c3","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.","apa":"Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no. 9. IOPscience, 2017.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (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.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3."},"date_created":"2018-12-11T11:48:41Z","type":"journal_article","external_id":{"isi":["000411842900001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"day":"26","oa":1,"status":"public","date_published":"2017-09-26T00:00:00Z","doi":"10.1088/1742-5468/aa85c3","intvolume":" 2017","isi":1,"article_number":"093404"},{"status":"public","publication_status":"published","doi":"10.18632/oncotarget.20914","publisher":"Impact Journals","date_published":"2017-09-15T00:00:00Z","intvolume":" 8","article_type":"original","_id":"8235","extern":"1","day":"15","main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.20914"}],"oa":1,"title":"Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials","page":"83128-83141","publication":"Oncotarget","year":"2017","oa_version":"Published Version","citation":{"ista":"Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M, Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 8, 83128–83141.","chicago":"Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914.","short":"J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann, F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget 8 (2017) 83128–83141.","ieee":"J. Singer et al., “Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals, pp. 83128–83141, 2017.","mla":"Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 83128–41, doi:10.18632/oncotarget.20914.","apa":"Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann, M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.20914","ama":"Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 2017;8:83128-83141. doi:10.18632/oncotarget.20914"},"date_created":"2020-08-10T11:53:18Z","type":"journal_article","volume":8,"article_processing_charge":"No","date_updated":"2021-01-12T08:17:39Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1949-2553"]},"author":[{"orcid":"0000-0002-8777-3502","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit"},{"full_name":"Berroterán-Infante, Neydher","last_name":"Berroterán-Infante","first_name":"Neydher"},{"first_name":"Christina","full_name":"Rami-Mark, Christina","last_name":"Rami-Mark"},{"first_name":"Monika","full_name":"Dumanic, Monika","last_name":"Dumanic"},{"first_name":"Miroslawa","last_name":"Matz","full_name":"Matz, Miroslawa"},{"full_name":"Willmann, Michael","last_name":"Willmann","first_name":"Michael"},{"first_name":"Fritz","last_name":"Andreae","full_name":"Andreae, Fritz"},{"last_name":"Singer","full_name":"Singer, Josef","first_name":"Josef"},{"last_name":"Wadsak","full_name":"Wadsak, Wolfgang","first_name":"Wolfgang"},{"full_name":"Mitterhauser, Markus","last_name":"Mitterhauser","first_name":"Markus"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"month":"09"},{"publisher":"Wiley","article_type":"original","_id":"8236","publication_status":"published","title":"AllergoOncology - the impact of allergy in oncology: EAACI position paper","page":"866-887","volume":72,"issue":"6","year":"2017","language":[{"iso":"eng"}],"author":[{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, E.","first_name":"E.","orcid":"0000-0003-4019-5765"},{"first_name":"H. J.","full_name":"Bax, H. J.","last_name":"Bax"},{"last_name":"Bianchini","full_name":"Bianchini, R.","first_name":"R."},{"full_name":"Capron, M.","last_name":"Capron","first_name":"M."},{"last_name":"Corrigan","full_name":"Corrigan, C.","first_name":"C."},{"first_name":"M.","last_name":"Castells","full_name":"Castells, M."},{"full_name":"Dombrowicz, D.","last_name":"Dombrowicz","first_name":"D."},{"first_name":"T. R.","last_name":"Daniels-Wells","full_name":"Daniels-Wells, T. R."},{"first_name":"Judit","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","orcid":"0000-0002-8777-3502"},{"first_name":"E.","full_name":"Fiebiger, E.","last_name":"Fiebiger"},{"first_name":"S.","last_name":"Gatault","full_name":"Gatault, S."},{"last_name":"Gould","full_name":"Gould, H. J.","first_name":"H. J."},{"last_name":"Janda","full_name":"Janda, J.","first_name":"J."},{"full_name":"Josephs, D. H.","last_name":"Josephs","first_name":"D. H."},{"first_name":"P.","last_name":"Karagiannis","full_name":"Karagiannis, P."},{"first_name":"F.","last_name":"Levi-Schaffer","full_name":"Levi-Schaffer, F."},{"full_name":"Meshcheryakova, A.","last_name":"Meshcheryakova","first_name":"A."},{"first_name":"D.","full_name":"Mechtcheriakova, D.","last_name":"Mechtcheriakova"},{"first_name":"Y.","full_name":"Mekori, Y.","last_name":"Mekori"},{"full_name":"Mungenast, F.","last_name":"Mungenast","first_name":"F."},{"full_name":"Nigro, E. A.","last_name":"Nigro","first_name":"E. A."},{"first_name":"M. L.","full_name":"Penichet, M. L.","last_name":"Penichet"},{"first_name":"F.","full_name":"Redegeld, F.","last_name":"Redegeld"},{"first_name":"L.","last_name":"Saul","full_name":"Saul, L."},{"first_name":"J.","full_name":"Singer, J.","last_name":"Singer"},{"full_name":"Spicer, J. F.","last_name":"Spicer","first_name":"J. F."},{"last_name":"Siccardi","full_name":"Siccardi, A. G.","first_name":"A. G."},{"first_name":"E.","full_name":"Spillner, E.","last_name":"Spillner"},{"last_name":"Turner","full_name":"Turner, M. C.","first_name":"M. C."},{"first_name":"E.","full_name":"Untersmayr, E.","last_name":"Untersmayr"},{"first_name":"L.","full_name":"Vangelista, L.","last_name":"Vangelista"},{"last_name":"Karagiannis","full_name":"Karagiannis, S. N.","first_name":"S. N."}],"publication_identifier":{"issn":["0105-4538"]},"article_processing_charge":"No","date_updated":"2021-01-12T08:17:39Z","abstract":[{"lang":"eng","text":"Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-06-01T00:00:00Z","doi":"10.1111/all.13119","intvolume":" 72","status":"public","extern":"1","main_file_link":[{"url":"https://doi.org/10.1111/all.13119","open_access":"1"}],"day":"01","oa":1,"type":"journal_article","publication":"Allergy","citation":{"chicago":"Jensen-Jarolim, E., H. J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” Allergy. Wiley, 2017. https://doi.org/10.1111/all.13119.","ista":"Jensen-Jarolim E, Bax HJ, Bianchini R, Capron M, Corrigan C, Castells M, Dombrowicz D, Daniels-Wells TR, Singer J, Fiebiger E, Gatault S, Gould HJ, Janda J, Josephs DH, Karagiannis P, Levi-Schaffer F, Meshcheryakova A, Mechtcheriakova D, Mekori Y, Mungenast F, Nigro EA, Penichet ML, Redegeld F, Saul L, Singer J, Spicer JF, Siccardi AG, Spillner E, Turner MC, Untersmayr E, Vangelista L, Karagiannis SN. 2017. AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. 72(6), 866–887.","ieee":"E. Jensen-Jarolim et al., “AllergoOncology - the impact of allergy in oncology: EAACI position paper,” Allergy, vol. 72, no. 6. Wiley, pp. 866–887, 2017.","short":"E. Jensen-Jarolim, H.J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, T.R. Daniels-Wells, J. Singer, E. Fiebiger, S. Gatault, H.J. Gould, J. Janda, D.H. Josephs, P. Karagiannis, F. Levi-Schaffer, A. Meshcheryakova, D. Mechtcheriakova, Y. Mekori, F. Mungenast, E.A. Nigro, M.L. Penichet, F. Redegeld, L. Saul, J. Singer, J.F. Spicer, A.G. Siccardi, E. Spillner, M.C. Turner, E. Untersmayr, L. Vangelista, S.N. Karagiannis, Allergy 72 (2017) 866–887.","mla":"Jensen-Jarolim, E., et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” Allergy, vol. 72, no. 6, Wiley, 2017, pp. 866–87, doi:10.1111/all.13119.","apa":"Jensen-Jarolim, E., Bax, H. J., Bianchini, R., Capron, M., Corrigan, C., Castells, M., … Karagiannis, S. N. (2017). AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. Wiley. https://doi.org/10.1111/all.13119","ama":"Jensen-Jarolim E, Bax HJ, Bianchini R, et al. AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. 2017;72(6):866-887. doi:10.1111/all.13119"},"oa_version":"Published Version","date_created":"2020-08-10T11:53:26Z","month":"06","quality_controlled":"1"},{"volume":8,"type":"journal_article","date_created":"2020-08-10T11:53:32Z","citation":{"ieee":"K. M. Ilieva et al., “Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields,” Frontiers in Immunology, vol. 8. Frontiers, 2017.","short":"K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli, H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs, A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis, Frontiers in Immunology 8 (2017).","ista":"Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J, Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 8, 1112.","chicago":"Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev, Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology. Frontiers, 2017. https://doi.org/10.3389/fimmu.2017.01112.","ama":"Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 2017;8. doi:10.3389/fimmu.2017.01112","apa":"Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli, S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2017.01112","mla":"Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” Frontiers in Immunology, vol. 8, 1112, Frontiers, 2017, doi:10.3389/fimmu.2017.01112."},"oa_version":"Published Version","publication":"Frontiers in Immunology","year":"2017","author":[{"last_name":"Ilieva","full_name":"Ilieva, Kristina M.","first_name":"Kristina M."},{"full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"first_name":"Daniela Y.","last_name":"Achkova","full_name":"Achkova, Daniela Y."},{"first_name":"Tihomir S.","full_name":"Dodev, Tihomir S.","last_name":"Dodev"},{"first_name":"Silvia","full_name":"Mele, Silvia","last_name":"Mele"},{"first_name":"Silvia","full_name":"Crescioli, Silvia","last_name":"Crescioli"},{"full_name":"Bax, Heather J.","last_name":"Bax","first_name":"Heather J."},{"first_name":"Anthony","full_name":"Cheung, Anthony","last_name":"Cheung"},{"first_name":"Panagiotis","full_name":"Karagiannis, Panagiotis","last_name":"Karagiannis"},{"first_name":"Isabel","last_name":"Correa","full_name":"Correa, Isabel"},{"full_name":"Figini, Mariangela","last_name":"Figini","first_name":"Mariangela"},{"first_name":"Rebecca","last_name":"Marlow","full_name":"Marlow, Rebecca"},{"full_name":"Josephs, Debra H.","last_name":"Josephs","first_name":"Debra H."},{"first_name":"Andrew J.","last_name":"Beavil","full_name":"Beavil, Andrew J."},{"first_name":"John","full_name":"Maher, John","last_name":"Maher"},{"full_name":"Spicer, James F.","last_name":"Spicer","first_name":"James F."},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"},{"last_name":"Tutt","full_name":"Tutt, Andrew N.","first_name":"Andrew N."},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"}],"month":"09","publication_identifier":{"issn":["1664-3224"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells.","lang":"eng"}],"quality_controlled":"1","date_updated":"2021-01-12T08:17:39Z","article_processing_charge":"No","_id":"8237","article_number":"1112","intvolume":" 8","article_type":"original","publisher":"Frontiers","doi":"10.3389/fimmu.2017.01112","date_published":"2017-09-11T00:00:00Z","publication_status":"published","status":"public","oa":1,"title":"Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3389/fimmu.2017.01112"}],"day":"11","extern":"1"},{"publication":"Scientific Reports","year":"2017","date_created":"2020-08-10T11:53:46Z","oa_version":"Published Version","citation":{"mla":"Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports, vol. 7, 45067, Springer Nature, 2017, doi:10.1038/srep45067.","apa":"Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C., Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. Springer Nature. https://doi.org/10.1038/srep45067","ama":"Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 2017;7. doi:10.1038/srep45067","chicago":"Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner, Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” Scientific Reports. Springer Nature, 2017. https://doi.org/10.1038/srep45067.","ista":"Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 7, 45067.","ieee":"F. Roth-Walter et al., “Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure,” Scientific Reports, vol. 7. Springer Nature, 2017.","short":"F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J. Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak, A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017)."},"volume":7,"type":"journal_article","quality_controlled":"1","date_updated":"2021-01-12T08:17:40Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk.","lang":"eng"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Roth-Walter, Franziska","last_name":"Roth-Walter","first_name":"Franziska"},{"first_name":"Cornelia","last_name":"Bergmayr","full_name":"Bergmayr, Cornelia"},{"first_name":"Sarah","last_name":"Meitz","full_name":"Meitz, Sarah"},{"last_name":"Buchleitner","full_name":"Buchleitner, Stefan","first_name":"Stefan"},{"full_name":"Stremnitzer, Caroline","last_name":"Stremnitzer","first_name":"Caroline"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas, Judit","last_name":"Fazekas","orcid":"0000-0002-8777-3502"},{"first_name":"Anna","full_name":"Moskovskich, Anna","last_name":"Moskovskich"},{"first_name":"Mario A.","last_name":"Müller","full_name":"Müller, Mario A."},{"full_name":"Roth, Georg A.","last_name":"Roth","first_name":"Georg A."},{"full_name":"Manzano-Szalai, Krisztina","last_name":"Manzano-Szalai","first_name":"Krisztina"},{"full_name":"Dvorak, Zdenek","last_name":"Dvorak","first_name":"Zdenek"},{"last_name":"Neunkirchner","full_name":"Neunkirchner, Alina","first_name":"Alina"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"publication_identifier":{"issn":["2045-2322"]},"month":"03","status":"public","publication_status":"published","article_type":"original","intvolume":" 7","date_published":"2017-03-23T00:00:00Z","doi":"10.1038/srep45067","publisher":"Springer Nature","_id":"8239","article_number":"45067","day":"23","main_file_link":[{"url":"https://doi.org/10.1038/srep45067","open_access":"1"}],"extern":"1","oa":1,"title":"Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure"},{"volume":827,"scopus_import":"1","year":"2017","publication_identifier":{"issn":["00221120"]},"author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"language":[{"iso":"eng"}],"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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-26T16:17:43Z","_id":"824","publisher":"Cambridge University Press","publist_id":"6824","publication_status":"published","title":"Heteroclinic path to spatially localized chaos in pipe flow","department":[{"_id":"BjHo"}],"type":"journal_article","oa_version":"Submitted Version","citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics, vol. 827, R1, Cambridge University Press, 2017, doi:10.1017/jfm.2017.516.","apa":"Budanur, N. B., & Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.516","ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 2017;827. doi:10.1017/jfm.2017.516","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.516.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” Journal of Fluid Mechanics, vol. 827. Cambridge University Press, 2017.","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017)."},"date_created":"2018-12-11T11:48:42Z","publication":"Journal of Fluid Mechanics","month":"08","quality_controlled":"1","isi":1,"article_number":"R1","doi":"10.1017/jfm.2017.516","date_published":"2017-08-18T00:00:00Z","intvolume":" 827","status":"public","oa":1,"external_id":{"isi":["000408326300001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.10484","open_access":"1"}],"day":"18"},{"type":"journal_article","volume":8,"citation":{"ama":"Singer J, Grunt TW, Jensen-Jarolim E, Singer J. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. 2017;8:35076-35087. doi:10.18632/oncotarget.16623","mla":"Singer, Judit, et al. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget, vol. 8, Impact Journals, 2017, pp. 35076–87, doi:10.18632/oncotarget.16623.","apa":"Singer, J., Grunt, T. W., Jensen-Jarolim, E., & Singer, J. (2017). Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.16623","short":"J. Singer, T.W. Grunt, E. Jensen-Jarolim, J. Singer, Oncotarget 8 (2017) 35076–35087.","ieee":"J. Singer, T. W. Grunt, E. Jensen-Jarolim, and J. Singer, “Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474,” Oncotarget, vol. 8. Impact Journals, pp. 35076–35087, 2017.","chicago":"Singer, Judit, Thomas W. Grunt, Erika Jensen-Jarolim, and Josef Singer. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.16623.","ista":"Singer J, Grunt TW, Jensen-Jarolim E, Singer J. 2017. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. 8, 35076–35087."},"oa_version":"Published Version","date_created":"2020-08-10T11:53:53Z","year":"2017","publication":"Oncotarget","publication_identifier":{"issn":["1949-2553"]},"month":"03","author":[{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas","full_name":"Fazekas, Judit","first_name":"Judit"},{"first_name":"Thomas W.","full_name":"Grunt, Thomas W.","last_name":"Grunt"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Background/Aim: Cancer cell lines are indispensible surrogate models in cancer research, as they can be used off-the-shelf, expanded to the desired extent, easily modified and exchanged between research groups for affirmation, reproduction or follow-up experiments.\r\nAs malignant cells are prone to genomic instability, phenotypical changes may occur after certain passages in culture. Thus, cell lines have to be regularly authenticated to ensure data quality. In between experiments these cell lines are often stored in liquid nitrogen for extended time periods.\r\nAlthough freezing of cells is a necessary evil, little research is performed on how long-term storage affects cancer cell lines. Therefore, this study investigated the effects of a 28-year long liquid nitrogen storage period on BT474 cells with regard to phenotypical changes, differences in cell-surface receptor expression as well as cytokine and gene expressional variations.\r\nMethods: Two batches of BT474 cells, one frozen in 1986, the other directly purchased from ATCC were investigated by light microscopy, cell growth analysis, flow cytometry and cytokine as well as whole-transcriptome expression profiling.\r\nResults: The cell lines were morphologically indifferent and showed similar growth rates and similar cell-surface receptor expression. Transcriptome analysis revealed significant differences in only 26 of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and 22 down-regulated.\r\nConclusion: This study demonstrates that even after very long periods of storage in liquid nitrogen, cancer cell lines display only minimal changes in their gene expression profiles. However, also such minor changes should be carefully assessed before continuation of experiments, especially if phenotypic alterations can be additionally observed."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2021-01-12T08:17:41Z","quality_controlled":"1","_id":"8240","date_published":"2017-03-28T00:00:00Z","doi":"10.18632/oncotarget.16623","publisher":"Impact Journals","intvolume":" 8","article_type":"original","publication_status":"published","status":"public","title":"Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474","page":"35076-35087","oa":1,"extern":"1","day":"28","main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.16623","open_access":"1"}]},{"day":"01","oa":1,"date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1678","intvolume":" 70","status":"public","month":"08","type":"journal_article","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","oa_version":"Published Version","citation":{"short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678.","ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678."},"date_created":"2018-12-11T11:48:42Z","title":"Metadata for research data in practice","page":"200 - 207","department":[{"_id":"E-Lib"}],"publisher":"VÖB","publist_id":"6823","_id":"825","file_date_updated":"2020-07-14T12:48:11Z","ddc":["020"],"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Barbara","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","orcid":"0000-0003-2724-4614"}],"publication_identifier":{"issn":["10222588"]},"file":[{"date_updated":"2020-07-14T12:48:11Z","file_name":"2017_VOEB_Petritsch.pdf","checksum":"7c4544d07efa2c2add8612b489abb4e2","date_created":"2019-01-18T13:32:17Z","file_size":7843975,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5850"}],"date_updated":"2021-01-12T08:17:44Z","abstract":[{"lang":"eng","text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":70,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"issue":"2","year":"2017"},{"publication":"Proceedings of the 26th USENIX Conference on Security Symposium","year":"2017","oa_version":"Published Version","citation":{"apa":"Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi, I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In Proceedings of the 26th USENIX Conference on Security Symposium (pp. 1271–1287). Vancouver, Canada: USENIX Association.","mla":"Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287.","ama":"Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In: Proceedings of the 26th USENIX Conference on Security Symposium. USENIX Association; 2017:1271–1287.","ista":"Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. Proceedings of the 26th USENIX Conference on Security Symposium. SEC: Security Symposium, 1271–1287.","chicago":"Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” In Proceedings of the 26th USENIX Conference on Security Symposium, 1271–1287. USENIX Association, 2017.","short":"K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi, J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287.","ieee":"K. Nikitin et al., “CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds,” in Proceedings of the 26th USENIX Conference on Security Symposium, Vancouver, Canada, 2017, pp. 1271–1287."},"date_created":"2020-08-26T12:04:44Z","type":"conference","article_processing_charge":"No","date_updated":"2021-01-12T08:18:00Z","quality_controlled":"1","abstract":[{"text":"Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that eliminates single points of failure, enforces transparency, and provides efficient verifiability of integrity and authenticity for software-release processes. Independent witness servers collectively verify conformance of software updates to release policies, build verifiers validate the source-to-binary correspondence, and a tamper-proof release log stores collectively signed updates, thus ensuring that no release is accepted by clients before being widely disclosed and validated. The release log embodies a skipchain, a novel data structure, enabling arbitrarily out-of-date clients to efficiently validate updates and signing keys. Evaluation of our CHAINIAC prototype on reproducible Debian packages shows that the automated update process takes the average of 5 minutes per release for individual packages, and only 20 seconds for the aggregate timeline. We further evaluate the framework using real-world data from the PyPI package repository and show that it offers clients security comparable to verifying every single update themselves while consuming only one-fifth of the bandwidth and having a minimal computational overhead.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"end_date":"2017-08-18","location":"Vancouver, Canada","start_date":"2017-08-16","name":"SEC: Security Symposium"},"author":[{"first_name":"Kirill","full_name":"Nikitin, Kirill","last_name":"Nikitin"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"last_name":"Jovanovic","full_name":"Jovanovic, Philipp","first_name":"Philipp"},{"first_name":"Linus","full_name":"Gasser, Linus","last_name":"Gasser"},{"first_name":"Nicolas","full_name":"Gailly, Nicolas","last_name":"Gailly"},{"last_name":"Khoffi","full_name":"Khoffi, Ismail","first_name":"Ismail"},{"last_name":"Cappos","full_name":"Cappos, Justin","first_name":"Justin"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"month":"09","publication_identifier":{"isbn":["9781931971409"]},"status":"public","publication_status":"published","date_published":"2017-09-01T00:00:00Z","publisher":"USENIX Association","_id":"8301","extern":"1","day":"01","main_file_link":[{"url":"https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf","open_access":"1"}],"title":"CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds","oa":1,"page":"1271–1287"},{"day":"01","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1067"}],"extern":"1","page":"444-460","title":"Scalable bias-resistant distributed randomness","oa":1,"publisher":"IEEE","doi":"10.1109/SP.2017.45","date_published":"2017-06-01T00:00:00Z","_id":"8306","status":"public","publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Syta","full_name":"Syta, E.","first_name":"E."},{"full_name":"Jovanovic, P.","last_name":"Jovanovic","first_name":"P."},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"N.","last_name":"Gailly","full_name":"Gailly, N."},{"first_name":"L.","last_name":"Gasser","full_name":"Gasser, L."},{"first_name":"I.","last_name":"Khoffi","full_name":"Khoffi, I."},{"first_name":"M. J.","full_name":"Fischer, M. J.","last_name":"Fischer"},{"full_name":"Ford, B.","last_name":"Ford","first_name":"B."}],"publication_identifier":{"issn":["2375-1207"],"isbn":["9781509055340"]},"conference":{"start_date":"2017-05-22","location":"San Jose, CA, United States","name":"SP: Symposium on Security and Privacy","end_date":"2017-05-26"},"month":"06","date_updated":"2021-01-12T08:18:02Z","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Bias-resistant public randomness is a critical component in many (distributed) protocols. Generating public randomness is hard, however, because active adversaries may behave dishonestly to bias public random choices toward their advantage. Existing solutions do not scale to hundreds or thousands of participants, as is needed in many decentralized systems. We propose two large-scale distributed protocols, RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted client to divide a set of randomness servers into groups for scalability, and it depends on the pigeonhole principle to ensure output integrity, even for non-random, adversarial group choices. RandHerd implements an efficient, decentralized randomness beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound in a one-time setup to arrange participants into verifiably unbiased random secret-sharing groups, which then repeatedly produce random output at predefined intervals. Our prototype demonstrates that RandHound and RandHerd achieve good performance across hundreds of participants while retaining a low failure probability by properly selecting protocol parameters, such as a group size and secret-sharing threshold. For example, when sharding 512 nodes into groups of 32, our experiments show that RandHound can produce fresh random output after 240 seconds. RandHerd, after a setup phase of 260 seconds, is able to generate fresh random output in intervals of approximately 6 seconds. For this configuration, both protocols operate at a failure probability of at most 0.08% against a Byzantine adversary."}],"type":"conference","year":"2017","publication":"2017 IEEE Symposium on Security and Privacy","date_created":"2020-08-26T12:26:08Z","oa_version":"Preprint","citation":{"short":"E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–460.","ieee":"E. Syta et al., “Scalable bias-resistant distributed randomness,” in 2017 IEEE Symposium on Security and Privacy, San Jose, CA, United States, 2017, pp. 444–460.","chicago":"Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.” In 2017 IEEE Symposium on Security and Privacy, 444–60. IEEE, 2017. https://doi.org/10.1109/SP.2017.45.","ista":"Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 444–460.","ama":"Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed randomness. In: 2017 IEEE Symposium on Security and Privacy. IEEE; 2017:444-460. doi:10.1109/SP.2017.45","apa":"Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi, I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In 2017 IEEE Symposium on Security and Privacy (pp. 444–460). San Jose, CA, United States: IEEE. https://doi.org/10.1109/SP.2017.45","mla":"Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–60, doi:10.1109/SP.2017.45."}},{"intvolume":" 10424","date_published":"2017-07-28T00:00:00Z","doi":"10.1007/978-3-319-64689-3_32","isi":1,"status":"public","day":"28","main_file_link":[{"url":"https://arxiv.org/abs/1705.02045","open_access":"1"}],"external_id":{"isi":["000432085900032"]},"oa":1,"editor":[{"full_name":"Felsberg, Michael","last_name":"Felsberg","first_name":"Michael"},{"first_name":"Anders","full_name":"Heyden, Anders","last_name":"Heyden"},{"first_name":"Norbert","full_name":"Krüger, Norbert","last_name":"Krüger"}],"type":"conference","date_created":"2018-12-11T11:48:45Z","citation":{"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. https://doi.org/10.1007/978-3-319-64689-3_32.","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.","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 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.","apa":"Heiss, T., & Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, & N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. https://doi.org/10.1007/978-3-319-64689-3_32","mla":"Heiss, Teresa, and Hubert Wagner. Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:10.1007/978-3-319-64689-3_32.","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:10.1007/978-3-319-64689-3_32"},"oa_version":"Submitted Version","month":"07","quality_controlled":"1","publist_id":"6815","publisher":"Springer","_id":"833","publication_status":"published","title":"Streaming algorithm for Euler characteristic curves of multidimensional images","page":"397 - 409","department":[{"_id":"HeEd"}],"alternative_title":["LNCS"],"volume":10424,"year":"2017","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"]},"conference":{"start_date":"2017-08-22","name":"CAIP: Computer Analysis of Images and Patterns","location":"Ystad, Sweden","end_date":"2017-08-24"},"author":[{"orcid":"0000-0002-1780-2689","first_name":"Teresa","last_name":"Heiss","full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-26T16:10:03Z","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}]},{"department":[{"_id":"MaSe"}],"title":"Thouless energy and multifractality across the many-body localization transition","publication_status":"published","publisher":"American Physical Society","publist_id":"6814","_id":"834","article_processing_charge":"No","date_updated":"2023-09-26T15:51:54Z","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699950"]},"author":[{"orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"first_name":"Papic","full_name":"Zlatko, Papic","last_name":"Zlatko"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"}],"issue":"10","scopus_import":"1","year":"2017","volume":96,"external_id":{"isi":["000409429300004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"day":"06","oa":1,"status":"public","doi":"10.1103/PhysRevB.96.104201","date_published":"2017-09-06T00:00:00Z","intvolume":" 96","isi":1,"article_number":"104201","quality_controlled":"1","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)","month":"09","publication":"Physical Review B - Condensed Matter and Materials Physics","oa_version":"Submitted Version","citation":{"short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10. American Physical Society, 2017.","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.","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.","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201","apa":"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. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201."},"date_created":"2018-12-11T11:48:45Z","type":"journal_article"},{"abstract":[{"lang":"eng","text":"An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","file":[{"file_size":3027104,"date_created":"2018-12-12T10:15:32Z","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"5153","relation":"main_file","file_name":"IST-2017-859-v1+1_ncomms15990.pdf","date_updated":"2020-07-14T12:48:12Z","checksum":"99a3d63308d4250eda0a35341171f80e"}],"date_updated":"2023-09-26T15:51:28Z","publication_identifier":{"issn":["20411723"]},"author":[{"last_name":"Makhijani","full_name":"Makhijani, Kalpana","first_name":"Kalpana"},{"last_name":"Alexander","full_name":"Alexander, Brandy","first_name":"Brandy"},{"first_name":"Deepti","last_name":"Rao","full_name":"Rao, Deepti"},{"last_name":"Petraki","full_name":"Petraki, Sophia","first_name":"Sophia"},{"first_name":"Leire","last_name":"Herboso","full_name":"Herboso, Leire"},{"first_name":"Katelyn","full_name":"Kukar, Katelyn","last_name":"Kukar"},{"first_name":"Itrat","full_name":"Batool, Itrat","last_name":"Batool"},{"first_name":"Stephanie","full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner"},{"first_name":"Katrina","full_name":"Gold, Katrina","last_name":"Gold"},{"first_name":"Corinna","last_name":"Wong","full_name":"Wong, Corinna"},{"last_name":"O'Connor","full_name":"O'Connor, Michael","first_name":"Michael"},{"last_name":"Brückner","full_name":"Brückner, Katja","first_name":"Katja"}],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2017","has_accepted_license":"1","volume":8,"title":"Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons","publication_status":"published","ddc":["570","576","616"],"file_date_updated":"2020-07-14T12:48:12Z","_id":"835","publisher":"Nature Publishing Group","publist_id":"6813","quality_controlled":"1","pubrep_id":"859","month":"07","citation":{"ama":"Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 2017;8. doi:10.1038/ncomms15990","mla":"Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8, 15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990.","apa":"Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15990","ieee":"K. Makhijani et al., “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017).","chicago":"Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990.","ista":"Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990."},"oa_version":"Published Version","date_created":"2018-12-11T11:48:45Z","publication":"Nature Communications","type":"journal_article","oa":1,"external_id":{"isi":["000406360100001"]},"extern":"1","day":"27","status":"public","isi":1,"article_number":"15990","doi":"10.1038/ncomms15990","date_published":"2017-07-27T00:00:00Z","intvolume":" 8"},{"day":"23","oa":1,"status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"5828","status":"public"}]},"doi":"10.15479/AT:ISTA:th_858","date_published":"2017-08-23T00:00:00Z","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. ","month":"08","pubrep_id":"858","degree_awarded":"PhD","oa_version":"Published Version","citation":{"ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","mla":"Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.","apa":"Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858"},"date_created":"2018-12-11T11:48:46Z","type":"dissertation","alternative_title":["ISTA Thesis"],"department":[{"_id":"JoCs"}],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"page":"93","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","publication_status":"published","file_date_updated":"2020-07-14T12:48:12Z","ddc":["571"],"publisher":"Institute of Science and Technology Austria","publist_id":"6811","_id":"837","article_processing_charge":"No","file":[{"file_size":3589490,"date_created":"2019-04-05T08:59:51Z","file_id":"6213","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dernst","checksum":"f11925fbbce31e495124b6bc4f10573c","file_name":"2017_Xu_Haibing_Thesis_Source.docx","date_updated":"2020-07-14T12:48:12Z"},{"checksum":"ffb10749a537d615fab1ef0937ccb157","file_name":"2017_Xu_Thesis_IST.pdf","date_updated":"2020-07-14T12:48:12Z","file_size":11668613,"date_created":"2019-04-05T08:59:51Z","file_id":"6214","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"date_updated":"2023-09-07T12:06:38Z","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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Haibing","last_name":"Xu"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2017","has_accepted_license":"1"},{"year":"2017","has_accepted_license":"1","date_updated":"2023-09-07T12:02:28Z","file":[{"date_created":"2018-12-12T10:10:13Z","file_size":847400,"relation":"main_file","file_id":"4799","creator":"system","content_type":"application/pdf","access_level":"open_access","checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_updated":"2020-07-14T12:48:12Z","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf"},{"checksum":"3462101745ce8ad199c2d0f75dae4a7e","date_updated":"2020-07-14T12:48:12Z","file_name":"2017_Thesis_Rybar_source.zip","date_created":"2019-04-05T08:24:11Z","file_size":26054879,"relation":"source_file","file_id":"6202","creator":"dernst","content_type":"application/zip","access_level":"closed"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 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. "}],"language":[{"iso":"eng"}],"author":[{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","full_name":"Rybar, Michal"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:12Z","ddc":["000"],"publist_id":"6810","publisher":"Institute of Science and Technology Austria","_id":"838","department":[{"_id":"KrPi"}],"alternative_title":["ISTA Thesis"],"page":"86","title":"(The exact security of) Message authentication codes","degree_awarded":"PhD","date_created":"2018-12-11T11:48:46Z","citation":{"ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828","apa":"Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828."},"oa_version":"Published Version","type":"dissertation","month":"06","pubrep_id":"828","status":"public","related_material":{"record":[{"status":"public","id":"2082","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6196","status":"public"}]},"date_published":"2017-06-26T00:00:00Z","doi":"10.15479/AT:ISTA:th_828","day":"26","oa":1},{"day":"14","oa":1,"doi":"10.15479/AT:ISTA:th_855","date_published":"2017-08-14T00:00:00Z","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1362"},{"id":"1633","relation":"part_of_dissertation","status":"public"},{"id":"5568","relation":"popular_science","status":"public"}]},"month":"08","pubrep_id":"855","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","type":"dissertation","degree_awarded":"PhD","citation":{"ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:10.15479/AT:ISTA:th_855","mla":"Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855.","apa":"Hahn, D. (2017). Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","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.","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855."},"oa_version":"Published Version","date_created":"2018-12-11T11:48:47Z","supervisor":[{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"title":"Brittle fracture simulation with boundary elements for computer graphics","page":"124","alternative_title":["ISTA Thesis"],"department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","publist_id":"6809","ec_funded":1,"_id":"839","file_date_updated":"2020-07-14T12:48:13Z","ddc":["004","005","006","531","621"],"publication_status":"published","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David","last_name":"Hahn","first_name":"David"}],"article_processing_charge":"No","file":[{"file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","date_updated":"2020-07-14T12:48:13Z","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","file_size":14596191,"date_created":"2018-12-12T10:14:46Z","access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"5100","relation":"main_file"},{"file_id":"6207","relation":"source_file","content_type":"application/zip","access_level":"closed","creator":"dernst","file_size":15060566,"date_created":"2019-04-05T08:40:30Z","checksum":"421672f68d563b029869c5cf1713f919","file_name":"2017_thesis_Hahn_source.zip","date_updated":"2020-07-14T12:48:13Z"}],"date_updated":"2024-02-21T13:48:02Z","abstract":[{"lang":"eng","text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"year":"2017"},{"isi":1,"intvolume":" 17","doi":"10.1021/acs.nanolett.7b02627","date_published":"2017-08-10T00:00:00Z","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"status":"public","relation":"dissertation_contains","id":"69"},{"relation":"dissertation_contains","id":"7996","status":"public"}]},"status":"public","oa":1,"day":"10","external_id":{"isi":["000411043500078"]},"type":"journal_article","date_created":"2018-12-11T11:48:47Z","oa_version":"Published Version","citation":{"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,” Nano Letters, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.","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.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627"},"publication":"Nano Letters","pubrep_id":"865","month":"08","quality_controlled":"1","_id":"840","ec_funded":1,"publist_id":"6808","publisher":"American Chemical Society","file_date_updated":"2020-07-14T12:48:13Z","ddc":["539"],"publication_status":"published","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","page":"5706 - 5710","project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"}],"department":[{"_id":"GeKa"}],"has_accepted_license":"1","volume":17,"acknowledged_ssus":[{"_id":"M-Shop"}],"year":"2017","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","issue":"9","publication_identifier":{"issn":["15306984"]},"author":[{"first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukusic","full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","first_name":"Hannes"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-09-26T15:50:22Z","file":[{"date_created":"2018-12-12T10:12:33Z","file_size":2449546,"creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4951","date_updated":"2020-07-14T12:48:13Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","checksum":"761371a0129b2aa442424b9561450ece"}],"article_processing_charge":"No"},{"article_type":"original","publisher":"Duke University Press","_id":"8423","publication_status":"published","page":"175-209","title":"On the marked length spectrum of generic strictly convex billiard tables","volume":167,"year":"2017","issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"author":[{"first_name":"Guan","last_name":"Huang","full_name":"Huang, Guan"},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"full_name":"Sorrentino, Alfonso","last_name":"Sorrentino","first_name":"Alfonso"}],"date_updated":"2021-01-12T08:19:11Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper we show that for a generic strictly convex domain, one can recover the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard map from the (maximal) marked length spectrum of the domain.","lang":"eng"}],"intvolume":" 167","date_published":"2017-12-08T00:00:00Z","doi":"10.1215/00127094-2017-0038","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.08838"}],"day":"08","external_id":{"arxiv":["1603.08838"]},"extern":"1","oa":1,"type":"journal_article","publication":"Duke Mathematical Journal","date_created":"2020-09-17T10:42:42Z","citation":{"ama":"Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 2017;167(1):175-209. doi:10.1215/00127094-2017-0038","apa":"Huang, G., Kaloshin, V., & Sorrentino, A. (2017). On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2017-0038","mla":"Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal, vol. 167, no. 1, Duke University Press, 2017, pp. 175–209, doi:10.1215/00127094-2017-0038.","short":"G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017) 175–209.","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of generic strictly convex billiard tables,” Duke Mathematical Journal, vol. 167, no. 1. Duke University Press, pp. 175–209, 2017.","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal. Duke University Press, 2017. https://doi.org/10.1215/00127094-2017-0038.","ista":"Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209."},"oa_version":"Preprint","arxiv":1,"month":"12","quality_controlled":"1"}]