[{"author":[{"full_name":"Arming, Sebastian","last_name":"Arming","first_name":"Sebastian"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen","full_name":"Katoen, Joost P"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"}],"month":"08","arxiv":1,"citation":{"ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., &#38; Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","mla":"Arming, Sebastian, et al. <i>Parameter-Independent Strategies for PMDPs via POMDPs</i>. Vol. 11024, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">10.1007/978-3-319-99154-2_4</a>.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-99154-2_4\">https://doi.org/10.1007/978-3-319-99154-2_4</a>.","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70."},"page":"53-70","_id":"79","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-99154-2_4","title":"Parameter-independent strategies for pMDPs via POMDPs","external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"isi":1,"day":"15","date_updated":"2023-09-13T09:38:28Z","conference":{"location":"Beijing, China","name":"QEST: Quantitative Evaluation of Systems","start_date":"2018-09-04","end_date":"2018-09-07"},"year":"2018","oa":1,"article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"date_created":"2018-12-11T11:44:31Z","abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"publist_id":"7975","status":"public","date_published":"2018-08-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     11024","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"quality_controlled":"1","publication_status":"published","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"type":"conference","volume":11024},{"citation":{"apa":"Cremer, S., Pull, C., &#38; Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. <i>Annual Review of Entomology</i>. 2018;63:105-123. doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:<a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">10.1146/annurev-ento-020117-043110</a>.","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” <i>Annual Review of Entomology</i>, vol. 63. Annual Reviews, pp. 105–123, 2018.","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” <i>Annual Review of Entomology</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-ento-020117-043110\">https://doi.org/10.1146/annurev-ento-020117-043110</a>."},"month":"01","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","last_name":"Pull"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias"}],"language":[{"iso":"eng"}],"_id":"806","page":"105 - 123","date_updated":"2023-09-19T09:29:45Z","publication_identifier":{"issn":["1545-4487"]},"day":"07","isi":1,"external_id":{"isi":["000424633700008"]},"title":"Social immunity: Emergence and evolution of colony-level disease protection","doi":"10.1146/annurev-ento-020117-043110","article_processing_charge":"No","year":"2018","related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"date_created":"2018-12-11T11:48:36Z","scopus_import":"1","oa_version":"None","intvolume":"        63","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2018-01-07T00:00:00Z","publication":"Annual Review of Entomology","publist_id":"6844","abstract":[{"text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology.","lang":"eng"}],"publisher":"Annual Reviews","publication_status":"published","quality_controlled":"1","department":[{"_id":"SyCr"}],"volume":63,"type":"journal_article"},{"file_date_updated":"2020-10-09T06:24:21Z","month":"08","file":[{"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","creator":"dernst","relation":"main_file","file_name":"2018_LNCS_Elgyuett.pdf","content_type":"application/pdf","date_created":"2020-10-09T06:24:21Z","date_updated":"2020-10-09T06:24:21Z","access_level":"open_access","file_id":"8638","success":1,"file_size":537219}],"author":[{"first_name":"Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>","apa":"Elgyütt, A., Ferrere, T., &#38; Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">https://doi.org/10.1007/978-3-030-00151-3_4</a>.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","mla":"Elgyütt, Adrian, et al. <i>Monitoring Temporal Logic with Clock Variables</i>. Vol. 11022, Springer, 2018, pp. 53–70, doi:<a href=\"https://doi.org/10.1007/978-3-030-00151-3_4\">10.1007/978-3-030-00151-3_4</a>."},"ddc":["000"],"page":"53 - 70","_id":"81","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000884993200004"]},"title":"Monitoring temporal logic with clock variables","doi":"10.1007/978-3-030-00151-3_4","date_updated":"2023-09-13T08:58:34Z","day":"26","year":"2018","has_accepted_license":"1","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Beijing, China","end_date":"2018-09-06","start_date":"2018-09-04"},"article_processing_charge":"No","oa":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:44:31Z","alternative_title":["LNCS"],"scopus_import":"1","date_published":"2018-08-26T00:00:00Z","status":"public","publist_id":"7973","abstract":[{"text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,","lang":"eng"}],"intvolume":"     11022","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"}],"quality_controlled":"1","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","volume":11022,"type":"conference"},{"ec_funded":1,"year":"2018","article_processing_charge":"No","oa":1,"isi":1,"external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","doi":"10.1016/j.cell.2018.06.033","date_updated":"2023-09-19T10:02:47Z","day":"12","issue":"2","page":"448 - 464.e24","acknowledgement":"In-Data-Review","language":[{"iso":"eng"}],"_id":"148","month":"07","author":[{"last_name":"Nishiyama","first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"last_name":"De Vries","first_name":"Jan","full_name":"De Vries, Jan"},{"full_name":"Buschmann, Henrik","first_name":"Henrik","last_name":"Buschmann"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"last_name":"Ullrich","first_name":"Kristian","full_name":"Ullrich, Kristian"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"full_name":"Lang, Daniel","last_name":"Lang","first_name":"Daniel"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"full_name":"Wilhelmsson, Per","last_name":"Wilhelmsson","first_name":"Per"},{"full_name":"Janitza, Philipp","last_name":"Janitza","first_name":"Philipp"},{"first_name":"Ramona","last_name":"Kern","full_name":"Kern, Ramona"},{"full_name":"Heyl, Alexander","last_name":"Heyl","first_name":"Alexander"},{"full_name":"Rümpler, Florian","first_name":"Florian","last_name":"Rümpler"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","first_name":"John","last_name":"Clay"},{"first_name":"Roman","last_name":"Skokan","full_name":"Skokan, Roman"},{"full_name":"Toyoda, Atsushi","last_name":"Toyoda","first_name":"Atsushi"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"first_name":"Hiroshi","last_name":"Kagoshima","full_name":"Kagoshima, Hiroshi"},{"full_name":"Schijlen, Elio","last_name":"Schijlen","first_name":"Elio"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"last_name":"Hetherington","first_name":"Alexander","full_name":"Hetherington, Alexander"},{"last_name":"Saltykova","first_name":"Assia","full_name":"Saltykova, Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"last_name":"Symeonidi","first_name":"Aikaterini","full_name":"Symeonidi, Aikaterini"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"last_name":"Van Nieuwerburgh","first_name":"Filip","full_name":"Van Nieuwerburgh, Filip"},{"last_name":"Deforce","first_name":"Dieter","full_name":"Deforce, Dieter"},{"full_name":"Chang, Caren","first_name":"Caren","last_name":"Chang"},{"last_name":"Karol","first_name":"Kenneth","full_name":"Karol, Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"last_name":"Ulvskov","first_name":"Peter","full_name":"Ulvskov, Peter"},{"last_name":"Glöckner","first_name":"Gernot","full_name":"Glöckner, Gernot"},{"full_name":"Delwiche, Charles","first_name":"Charles","last_name":"Delwiche"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Van De Peer, Yves","first_name":"Yves","last_name":"Van De Peer"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"first_name":"Liam","last_name":"Dolan","full_name":"Dolan, Liam"},{"first_name":"Yuji","last_name":"Kohara","full_name":"Kohara, Yuji"},{"first_name":"Sumio","last_name":"Sugano","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"last_name":"Delaux","first_name":"Pierre Marc","full_name":"Delaux, Pierre Marc"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"full_name":"Theissen, Gunter","last_name":"Theissen","first_name":"Gunter"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"first_name":"Jesper","last_name":"Harholt","full_name":"Harholt, Jesper"},{"last_name":"Dunand","first_name":"Christophe","full_name":"Dunand, Christophe"},{"full_name":"Zachgo, Sabine","first_name":"Sabine","last_name":"Zachgo"},{"first_name":"Jane","last_name":"Langdale","full_name":"Langdale, Jane"},{"full_name":"Maumus, Florian","last_name":"Maumus","first_name":"Florian"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"full_name":"Gould, Sven B","last_name":"Gould","first_name":"Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"citation":{"mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>.","ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>"},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"volume":174,"type":"journal_article","pmid":1,"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","status":"public","date_published":"2018-07-12T00:00:00Z","publication":"Cell","publist_id":"7774","abstract":[{"lang":"eng","text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote."}],"intvolume":"       174","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:44:53Z","scopus_import":"1"},{"abstract":[{"text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations.","lang":"eng"}],"status":"public","date_published":"2018-07-12T00:00:00Z","publist_id":"7772","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:44:53Z","type":"dissertation","department":[{"_id":"LaEr"}],"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","page":"456","degree_awarded":"PhD","language":[{"iso":"eng"}],"_id":"149","pubrep_id":"1040","month":"07","file_date_updated":"2020-07-14T12:44:57Z","author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":5801709,"file_id":"6241","access_level":"open_access","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","content_type":"application/pdf","relation":"main_file","file_name":"2018_thesis_Alt.pdf","checksum":"d4dad55a7513f345706aaaba90cb1bb8","creator":"dernst"},{"file_size":3802059,"file_id":"6242","access_level":"closed","date_created":"2019-04-08T13:55:20Z","date_updated":"2020-07-14T12:44:57Z","content_type":"application/zip","file_name":"2018_thesis_Alt_source.zip","relation":"source_file","creator":"dernst","checksum":"d73fcf46300dce74c403f2b491148ab4"}],"citation":{"chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","mla":"Alt, Johannes. <i>Dyson Equation and Eigenvalue Statistics of Random Matrices</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","apa":"Alt, J. (2018). <i>Dyson equation and eigenvalue statistics of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>"},"ddc":["515","519"],"has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1677"},{"status":"public","id":"550","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6183","status":"public"},{"relation":"part_of_dissertation","id":"566","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1010"},{"status":"public","relation":"part_of_dissertation","id":"6240"},{"id":"6184","relation":"part_of_dissertation","status":"public"}]},"year":"2018","ec_funded":1,"article_processing_charge":"No","oa":1,"title":"Dyson equation and eigenvalue statistics of random matrices","doi":"10.15479/AT:ISTA:TH_1040","publication_identifier":{"issn":["2663-337X"]},"day":"12","date_updated":"2024-02-22T14:34:33Z"},{"author":[{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav","orcid":"0000-0002-6625-3348"},{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723"},{"last_name":"Abe","first_name":"Jun","full_name":"Abe, Jun"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stein, Jens","first_name":"Jens","last_name":"Stein"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"month":"05","citation":{"ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. 2018;19(6):606-616. doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","ieee":"M. Hons <i>et al.</i>, “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” <i>Nature Immunology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>.","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616."},"page":"606 - 616","issue":"6","language":[{"iso":"eng"}],"_id":"15","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","doi":"10.1038/s41590-018-0109-z","title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","external_id":{"isi":["000433041500026"],"pmid":["29777221"]},"isi":1,"day":"18","date_updated":"2024-03-25T23:30:22Z","related_material":{"record":[{"status":"public","id":"6891","relation":"dissertation_contains"}]},"ec_funded":1,"year":"2018","article_processing_charge":"No","oa":1,"oa_version":"Published Version","scopus_import":"1","date_created":"2018-12-11T11:44:10Z","abstract":[{"lang":"eng","text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux."}],"publication":"Nature Immunology","publist_id":"8040","date_published":"2018-05-18T00:00:00Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        19","department":[{"_id":"MiSi"},{"_id":"Bio"}],"quality_controlled":"1","pmid":1,"project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"},{"grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration"},{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"publication_status":"published","publisher":"Nature Publishing Group","acknowledged_ssus":[{"_id":"SSU"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221","open_access":"1"}],"type":"journal_article","volume":19},{"volume":560,"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"FlSc"}],"pmid":1,"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       560","abstract":[{"lang":"eng","text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1."}],"status":"public","date_published":"2018-08-29T00:00:00Z","publication":"Nature","scopus_import":"1","date_created":"2018-12-11T11:44:53Z","oa_version":"Submitted Version","article_processing_charge":"No","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"year":"2018","publication_identifier":{"eissn":["1476-4687"]},"day":"29","date_updated":"2023-09-12T07:44:37Z","title":"Inositol phosphates are assembly co-factors for HIV-1","doi":"10.1038/s41586-018-0396-4","isi":1,"external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"language":[{"iso":"eng"}],"_id":"150","page":"509–512","issue":"7719","article_type":"original","citation":{"apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>."},"month":"08","author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"full_name":"Zadrozny, Kaneil K","first_name":"Kaneil K","last_name":"Zadrozny"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Terri D","last_name":"Lyddon","full_name":"Lyddon, Terri D"},{"full_name":"Ricana, Clifton L","last_name":"Ricana","first_name":"Clifton L"},{"first_name":"Jonathan M","last_name":"Wagner","full_name":"Wagner, Jonathan M"},{"full_name":"Perilla, Juan R","first_name":"Juan R","last_name":"Perilla"},{"first_name":"Pornillos Barbie K","last_name":"Ganser","full_name":"Ganser, Pornillos Barbie K"},{"last_name":"Johnson","first_name":"Marc C","full_name":"Johnson, Marc C"},{"last_name":"Pornillos","first_name":"Owen","full_name":"Pornillos, Owen"},{"last_name":"Vogt","first_name":"Volker","full_name":"Vogt, Volker"}]},{"oa_version":"Submitted Version","date_created":"2018-12-11T11:44:54Z","scopus_import":"1","status":"public","date_published":"2018-07-26T00:00:00Z","publication":"Trends in Cell Biology","publist_id":"7769","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"intvolume":"        28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","department":[{"_id":"LeSa"}],"publisher":"Elsevier","publication_status":"published","volume":28,"type":"journal_article","month":"07","file_date_updated":"2020-07-14T12:45:00Z","file":[{"file_id":"6994","file_size":2185385,"date_updated":"2020-07-14T12:45:00Z","date_created":"2019-11-07T12:55:20Z","access_level":"open_access","content_type":"application/pdf","creator":"lsazanov","checksum":"ef6d2b4e1fd63948539639242610bfa6","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","relation":"main_file"}],"author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867."},"ddc":["572"],"article_type":"original","issue":"10","page":"835 - 867","language":[{"iso":"eng"}],"_id":"152","isi":1,"external_id":{"isi":["000445118200007"]},"title":"Mammalian mitochondrial complex I structure and disease causing mutations","doi":"10.1016/j.tcb.2018.06.006","date_updated":"2023-09-13T08:51:56Z","day":"26","year":"2018","has_accepted_license":"1","article_processing_charge":"No","oa":1},{"date_updated":"2023-09-13T08:56:35Z","publication_identifier":{"issn":["0091679X"]},"day":"27","isi":1,"external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","doi":"10.1016/bs.mcb.2018.07.004","article_processing_charge":"No","year":"2018","citation":{"apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>."},"month":"07","author":[{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"language":[{"iso":"eng"}],"_id":"153","page":"79 - 91","publisher":"Academic Press","publication_status":"published","pmid":1,"quality_controlled":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"volume":147,"type":"book_chapter","date_created":"2018-12-11T11:44:54Z","scopus_import":"1","oa_version":"None","intvolume":"       147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2018-07-27T00:00:00Z","publication":"Methods in Cell Biology","publist_id":"7768","abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}]},{"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","_id":"154","language":[{"iso":"eng"}],"issue":"3","citation":{"ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3. Springer, 2018.","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3, 19, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>.","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. 2018;21(3). doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>","apa":"Moser, T., &#38; Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"ddc":["530"],"article_type":"original","file_date_updated":"2020-07-14T12:45:01Z","month":"09","article_number":"19","file":[{"content_type":"application/pdf","file_name":"2018_MathPhysics_Moser.pdf","relation":"main_file","checksum":"411c4db5700d7297c9cd8ebc5dd29091","creator":"dernst","file_size":496973,"file_id":"5729","access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-17T16:49:02Z"}],"author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","first_name":"Thomas"},{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"oa":1,"article_processing_charge":"No","year":"2018","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"52","status":"public"}]},"has_accepted_license":"1","date_updated":"2023-09-19T09:31:15Z","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"day":"01","isi":1,"external_id":{"isi":["000439639700001"]},"title":"Stability of the 2+2 fermionic system with point interactions","doi":"10.1007/s11040-018-9275-3","intvolume":"        21","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2018-09-01T00:00:00Z","publication":"Mathematical Physics Analysis and Geometry","publist_id":"7767","abstract":[{"lang":"eng","text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system."}],"date_created":"2018-12-11T11:44:55Z","scopus_import":"1","oa_version":"Published Version","volume":21,"type":"journal_article","publisher":"Springer","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"quality_controlled":"1","department":[{"_id":"RoSe"}]},{"language":[{"iso":"eng"}],"_id":"155","author":[{"full_name":"Xuereb, André","first_name":"André","last_name":"Xuereb"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"last_name":"Barzanjeh","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"}],"month":"05","article_number":"106721N","citation":{"chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>"},"arxiv":1,"conference":{"location":"Strasbourg, France","name":"SPIE: The international society for optical engineering","start_date":"2018-04-22","end_date":"2018-04-26"},"year":"2018","article_processing_charge":"No","oa":1,"doi":"10.1117/12.2309928","title":"Routing thermal noise through quantum networks","external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"isi":1,"day":"04","date_updated":"2023-09-18T08:12:24Z","abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"publist_id":"7766","status":"public","date_published":"2018-05-04T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     10672","oa_version":"Preprint","scopus_import":"1","alternative_title":["Proceedings of SPIE"],"date_created":"2018-12-11T11:44:55Z","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"type":"conference","volume":10672,"editor":[{"first_name":"D L","last_name":"Andrews","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"first_name":"A J","last_name":"Bain","full_name":"Bain, A J"},{"full_name":"Nunzi, J M","last_name":"Nunzi","first_name":"J M"}],"department":[{"_id":"JoFi"}],"quality_controlled":"1","publication_status":"published","publisher":"SPIE"},{"year":"2018","conference":{"start_date":"2018-07-15","end_date":"2018-07-17","location":"Oxford, UK","name":"FM: International Symposium on Formal Methods"},"has_accepted_license":"1","oa":1,"article_processing_charge":"No","external_id":{"isi":["000489765800009"]},"isi":1,"doi":"10.1007/978-3-319-95582-7_9","title":"The compound interest in relaxing punctuality","date_updated":"2023-09-19T10:05:37Z","day":"12","page":"147 - 164","language":[{"iso":"eng"}],"_id":"156","author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"}],"file":[{"file_size":485576,"file_id":"8637","success":1,"access_level":"open_access","date_created":"2020-10-09T06:22:41Z","date_updated":"2020-10-09T06:22:41Z","content_type":"application/pdf","file_name":"2018_LNCS_Ferrere.pdf","relation":"main_file","creator":"dernst","checksum":"a045c213c42c445f1889326f8db82a0a"}],"month":"07","file_date_updated":"2020-10-09T06:22:41Z","ddc":["000"],"citation":{"mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>"},"type":"conference","volume":10951,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","publist_id":"7765","status":"public","date_published":"2018-07-12T00:00:00Z","abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"intvolume":"     10951","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:55Z","scopus_import":"1","alternative_title":["LNCS"]},{"date_published":"2018-07-04T00:00:00Z","status":"public","publication":"Nature","publist_id":"7764","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"intvolume":"       559","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:56Z","scopus_import":"1","volume":559,"type":"journal_article","project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","issue":"7713","page":"246 - 249","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","_id":"157","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:02Z","month":"07","file":[{"relation":"main_file","file_name":"2018_Nature_Hilbe.pdf","creator":"dernst","checksum":"011ab905cf9a410bc2b96f15174d654d","content_type":"application/pdf","access_level":"open_access","date_created":"2019-11-19T08:09:57Z","date_updated":"2020-07-14T12:45:02Z","file_size":2834442,"file_id":"7049"}],"author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"first_name":"Štepán","last_name":"Šimsa","full_name":"Šimsa, Štepán"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"citation":{"ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>.","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249."},"ddc":["000"],"ec_funded":1,"year":"2018","has_accepted_license":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/engineering-cooperation/"}]},"article_processing_charge":"No","oa":1,"isi":1,"external_id":{"isi":["000438240900054"]},"title":"Evolution of cooperation in stochastic games","doi":"10.1038/s41586-018-0277-x","date_updated":"2023-09-11T13:43:22Z","day":"04"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"volume":4,"type":"journal_article","pmid":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","status":"public","date_published":"2018-07-16T00:00:00Z","publist_id":"7763","publication":"Nature Plants","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"intvolume":"         4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_created":"2018-12-11T11:44:56Z","scopus_import":"1","year":"2018","ec_funded":1,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"oa":1,"article_processing_charge":"No","isi":1,"external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","doi":"10.1038/s41477-018-0204-z","date_updated":"2025-05-07T11:12:31Z","day":"16","issue":"8","page":"548 - 553","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","_id":"158","language":[{"iso":"eng"}],"month":"07","author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"last_name":"Park","first_name":"Chulmin","full_name":"Park, Chulmin"},{"full_name":"Gutièrrez, Carla","last_name":"Gutièrrez","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska","first_name":"Barbara"},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Chen, Junyi","first_name":"Junyi","last_name":"Chen"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Laux","first_name":"Thomas","full_name":"Laux, Thomas"}],"citation":{"ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>.","ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018."}},{"day":"16","date_updated":"2023-09-13T09:36:35Z","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","doi":"10.1038/s41589-018-0090-8","isi":1,"external_id":{"isi":["000438970200010"]},"article_processing_charge":"No","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"has_accepted_license":"1","year":"2018","article_type":"original","citation":{"chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>.","ieee":"T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767. doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>"},"ddc":["570"],"file_date_updated":"2020-07-14T12:45:03Z","month":"07","file":[{"checksum":"d42935094ec845f54a0688bf12986d62","creator":"dernst","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-14T12:14:09Z","date_updated":"2020-07-14T12:45:03Z","access_level":"open_access","file_id":"7832","file_size":6321000}],"author":[{"full_name":"Fehrentz, Timm","last_name":"Fehrentz","first_name":"Timm"},{"last_name":"Huber","first_name":"Florian","full_name":"Huber, Florian"},{"last_name":"Hartrampf","first_name":"Nina","full_name":"Hartrampf, Nina"},{"full_name":"Bruegmann, Tobias","first_name":"Tobias","last_name":"Bruegmann"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"full_name":"Fine, Nicholas","last_name":"Fine","first_name":"Nicholas"},{"first_name":"Daniela","last_name":"Malan","full_name":"Malan, Daniela"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Tikhonov","first_name":"Denis","full_name":"Tikhonov, Denis"},{"last_name":"Sumser","first_name":"Maritn","full_name":"Sumser, Maritn"},{"first_name":"Philipp","last_name":"Sasse","full_name":"Sasse, Philipp"},{"full_name":"Hodson, David","last_name":"Hodson","first_name":"David"},{"full_name":"Zhorov, Boris","first_name":"Boris","last_name":"Zhorov"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"first_name":"Dirk","last_name":"Trauner","full_name":"Trauner, Dirk"}],"_id":"159","language":[{"iso":"eng"}],"page":"764 - 767","issue":"8","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoDa"}],"quality_controlled":"1","volume":14,"type":"journal_article","scopus_import":"1","date_created":"2018-12-11T11:44:56Z","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        14","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"date_published":"2018-07-16T00:00:00Z","status":"public","publication":"Nature Chemical Biology","publist_id":"7762"},{"date_updated":"2023-09-13T08:57:05Z","day":"16","external_id":{"isi":["000447469200001"]},"isi":1,"doi":"10.1103/PhysRevFluids.3.103303","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","oa":1,"article_processing_charge":"No","year":"2018","ec_funded":1,"has_accepted_license":"1","ddc":["532"],"citation":{"ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>."},"article_type":"original","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:04Z","date_created":"2018-12-12T10:13:56Z","file_size":1838431,"file_id":"5043","relation":"main_file","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","creator":"system","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","content_type":"application/pdf"}],"author":[{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999"},{"full_name":"Steinberg, Victor","first_name":"Victor","last_name":"Steinberg"}],"file_date_updated":"2020-07-14T12:45:04Z","month":"10","article_number":"103303","_id":"16","language":[{"iso":"eng"}],"pubrep_id":"1062","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","issue":"10","publisher":"American Physical Society","publication_status":"published","quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"department":[{"_id":"BjHo"}],"type":"journal_article","volume":3,"date_created":"2018-12-11T11:44:10Z","scopus_import":"1","oa_version":"Submitted Version","intvolume":"         3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Physical Review Fluids","publist_id":"8039","status":"public","date_published":"2018-10-16T00:00:00Z","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}]},{"date_created":"2018-12-11T11:44:57Z","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"     10981","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-18T00:00:00Z","status":"public","publist_id":"7761","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"publisher":"Springer","publication_status":"published","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","department":[{"_id":"ToHe"}],"volume":10981,"type":"conference","citation":{"ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102."},"ddc":["000"],"month":"07","file_date_updated":"2020-07-14T12:45:04Z","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"}],"file":[{"content_type":"application/pdf","file_name":"2018_LNCS_Kragl.pdf","relation":"main_file","checksum":"c64fff560fe5a7532ec10626ad1c215e","creator":"dernst","file_size":1603844,"file_id":"5705","access_level":"open_access","date_created":"2018-12-17T12:52:12Z","date_updated":"2020-07-14T12:45:04Z"}],"_id":"160","language":[{"iso":"eng"}],"page":"79 - 102","date_updated":"2023-09-13T08:45:09Z","day":"18","isi":1,"external_id":{"isi":["000491481600005"]},"title":"Layered Concurrent Programs","doi":"10.1007/978-3-319-96145-3_5","oa":1,"article_processing_charge":"No","year":"2018","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8332"}]},"conference":{"end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification","location":"Oxford, UK"}},{"citation":{"mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>"},"ddc":["570"],"file_date_updated":"2020-07-14T12:45:06Z","article_number":"2988","month":"07","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"},{"last_name":"Mc","first_name":"Andersson Anna","full_name":"Mc, Andersson Anna"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"file":[{"file_id":"5728","file_size":1043205,"date_updated":"2020-07-14T12:45:06Z","date_created":"2018-12-17T16:44:28Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","relation":"main_file","file_name":"2018_NatureComm_DeMartino.pdf"}],"language":[{"iso":"eng"}],"_id":"161","issue":"1","day":"30","date_updated":"2024-02-21T13:45:39Z","title":"Statistical mechanics for metabolic networks during steady state growth","doi":"10.1038/s41467-018-05417-9","isi":1,"external_id":{"isi":["000440149300021"]},"article_processing_charge":"No","oa":1,"related_material":{"record":[{"relation":"popular_science","id":"5587","status":"public"}]},"has_accepted_license":"1","ec_funded":1,"year":"2018","scopus_import":"1","date_created":"2018-12-11T11:44:57Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"date_published":"2018-07-30T00:00:00Z","status":"public","publication":"Nature Communications","publist_id":"7760","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","volume":9,"type":"journal_article"},{"_id":"162","language":[{"iso":"eng"}],"article_number":"e34465","file_date_updated":"2020-07-14T12:45:07Z","month":"06","file":[{"access_level":"open_access","date_created":"2018-12-17T16:41:58Z","date_updated":"2020-07-14T12:45:07Z","file_size":9816484,"file_id":"5727","file_name":"2018_eLife_Kaucka.pdf","relation":"main_file","checksum":"da2378cdcf6b5461dcde194e4d608343","creator":"dernst","content_type":"application/pdf"}],"author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"first_name":"Maria","last_name":"Kastriti","full_name":"Kastriti, Maria"},{"last_name":"Xie","first_name":"Meng","full_name":"Xie, Meng"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"first_name":"Maria","last_name":"Kasper","full_name":"Kasper, Maria"},{"first_name":"Orsolya","last_name":"Symmons","full_name":"Symmons, Orsolya"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"first_name":"Michael P","last_name":"Matise","full_name":"Matise, Michael P"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"last_name":"Fried","first_name":"Kaj","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"citation":{"ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465."},"ddc":["571"],"has_accepted_license":"1","related_material":{"record":[{"id":"9838","relation":"research_data","status":"public"}]},"ec_funded":1,"year":"2018","oa":1,"article_processing_charge":"No","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","doi":"10.7554/eLife.34465","isi":1,"external_id":{"isi":["000436227500001"]},"day":"13","date_updated":"2023-09-18T09:29:07Z","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"date_published":"2018-06-13T00:00:00Z","status":"public","publist_id":"7759","publication":"eLife","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         7","oa_version":"Published Version","scopus_import":"1","date_created":"2018-12-11T11:44:57Z","volume":7,"type":"journal_article","department":[{"_id":"AnKi"}],"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020"}],"quality_controlled":"1","publication_status":"published","publisher":"eLife Sciences Publications"},{"volume":66,"type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"publisher":"SAGE Publications","publication_status":"published","pmid":1,"quality_controlled":"1","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"intvolume":"        66","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2018-12-01T00:00:00Z","publication":"Journal of Histochemistry and Cytochemistry","abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"date_created":"2018-12-11T11:44:57Z","scopus_import":"1","oa_version":"Published Version","article_processing_charge":"No","oa":1,"year":"2018","date_updated":"2023-10-17T08:42:24Z","publication_identifier":{"issn":["0022-1554"]},"day":"01","isi":1,"external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","doi":"10.1369/0022155418786698","_id":"163","language":[{"iso":"eng"}],"issue":"12","page":"903-921","citation":{"ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921."},"article_type":"original","month":"12","author":[{"first_name":"Siegfried","last_name":"Reipert","full_name":"Reipert, Siegfried"},{"full_name":"Goldammer, Helmuth","last_name":"Goldammer","first_name":"Helmuth"},{"last_name":"Richardson","first_name":"Christine","full_name":"Richardson, Christine"},{"full_name":"Goldberg, Martin","last_name":"Goldberg","first_name":"Martin"},{"first_name":"Timothy","last_name":"Hawkins","full_name":"Hawkins, Timothy"},{"id":"3C054040-F248-11E8-B48F-1D18A9856A87","last_name":"Hollergschwandtner","first_name":"Elena","full_name":"Hollergschwandtner, Elena"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"last_name":"Antreich","first_name":"Sebastian","full_name":"Antreich, Sebastian"},{"first_name":"York","last_name":"Stierhof","full_name":"Stierhof, York"}]}]