[{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","publist_id":"6048","publisher":"Taylor & Francis","has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"citation":{"mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” <i>Computer-Aided Design and Applications</i>, vol. 13, no. 5, Taylor &#38; Francis, 2016, pp. 712–21, doi:<a href=\"https://doi.org/10.1080/16864360.2016.1150718\">10.1080/16864360.2016.1150718</a>.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” <i>Computer-Aided Design and Applications</i>, vol. 13, no. 5. Taylor &#38; Francis, pp. 712–721, 2016.","chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” <i>Computer-Aided Design and Applications</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/16864360.2016.1150718\">https://doi.org/10.1080/16864360.2016.1150718</a>.","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. <i>Computer-Aided Design and Applications</i>. 2016;13(5):712-721. doi:<a href=\"https://doi.org/10.1080/16864360.2016.1150718\">10.1080/16864360.2016.1150718</a>","apa":"Held, M., Huber, S., &#38; Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. <i>Computer-Aided Design and Applications</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/16864360.2016.1150718\">https://doi.org/10.1080/16864360.2016.1150718</a>"},"_id":"1272","oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:42Z","title":"Generalized offsetting of planar structures using skeletons","intvolume":"        13","ddc":["004","516"],"publication":"Computer-Aided Design and Applications","type":"journal_article","scopus_import":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams."}],"date_updated":"2026-07-07T05:34:31Z","oa":1,"volume":13,"doi":"10.1080/16864360.2016.1150718","date_published":"2016-09-02T00:00:00Z","article_processing_charge":"No","file":[{"file_id":"5206","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","relation":"main_file","date_created":"2018-12-12T10:16:20Z","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","creator":"system","content_type":"application/pdf","file_size":1678369}],"page":"712 - 721","date_created":"2018-12-11T11:51:04Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"full_name":"Huber, Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Palfrader","full_name":"Palfrader, Peter","first_name":"Peter"}],"das_tickbox":"1","issue":"5","month":"09","year":"2016","pubrep_id":"694"},{"date_published":"2016-04-02T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-07T05:34:16Z","oa":1,"volume":25,"doi":"10.1080/10586458.2015.1048011","quality_controlled":"1","abstract":[{"text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.","lang":"eng"}],"ec_funded":1,"corr_author":"1","intvolume":"        25","publication":"Experimental Mathematics","arxiv":1,"type":"journal_article","scopus_import":"1","year":"2016","das_tickbox":"1","issue":"2","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.00116"}],"page":"116 - 124","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:58Z","department":[{"_id":"HeEd"}],"author":[{"full_name":"Golmakani, Ali","last_name":"Golmakani","first_name":"Ali"},{"last_name":"Luzzatto","full_name":"Luzzatto, Stefano","first_name":"Stefano"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"external_id":{"arxiv":["1504.00116"],"isi":["000372490500002"]},"publisher":"Taylor & Francis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"02","acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The  authors  gratefully  acknowledge  the  Department  of\r\nMathematics  of  Kyoto  University  for  providing  access\r\nto  their  server  for  conducting  computations  for  this\r\nproject.","publist_id":"6071","publication_status":"published","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","_id":"1254","oa_version":"Preprint","project":[{"grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps"}],"citation":{"ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. 2016;25(2):116-124. doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>","apa":"Golmakani, A., Luzzatto, S., &#38; Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>, vol. 25, no. 2, Taylor &#38; Francis, 2016, pp. 116–24, doi:<a href=\"https://doi.org/10.1080/10586458.2015.1048011\">10.1080/10586458.2015.1048011</a>.","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” <i>Experimental Mathematics</i>, vol. 25, no. 2. Taylor &#38; Francis, pp. 116–124, 2016.","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/10586458.2015.1048011\">https://doi.org/10.1080/10586458.2015.1048011</a>.","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124."}},{"type":"journal_article","scopus_import":"1","arxiv":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","intvolume":"      2016","abstract":[{"lang":"eng","text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations."}],"ec_funded":1,"quality_controlled":"1","doi":"10.1088/1742-5468/aa4e8f","volume":2016,"oa":1,"date_updated":"2026-07-07T13:11:22Z","article_processing_charge":"No","date_published":"2016-12-30T00:00:00Z","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706"},{"first_name":"Davide","full_name":"Masoero, Davide","last_name":"Masoero"}],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:50:37Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1606.09048","open_access":"1"}],"month":"12","issue":"12","das_tickbox":"1","year":"2016","publication_status":"published","publist_id":"6165","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","status":"public","publisher":"IOP Publishing","article_number":"123502","external_id":{"arxiv":["1606.09048"],"isi":["000391973900001"]},"isi":1,"citation":{"apa":"De Martino, D., &#38; Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2016;2016(12). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12. IOP Publishing, 2016.","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2016. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>.","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"_id":"1188","oa_version":"Preprint","title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth"},{"title":"A phytochrome sensory domain permits receptor activation by red light","file_date_updated":"2020-07-14T12:44:55Z","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"_id":"1441","oa_version":"Submitted Version","citation":{"short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie International Edition 55 (2016) 6339–6342.","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>.","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 55(21), 6339–6342.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>"},"related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"}]},"external_id":{"isi":["000377918400039"]},"isi":1,"has_accepted_license":"1","status":"public","publisher":"Wiley","publist_id":"5755","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","publication_status":"published","pubrep_id":"840","year":"2016","month":"05","issue":"21","das_tickbox":"1","author":[{"orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy","first_name":"Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine","last_name":"Mckenzie"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"department":[{"_id":"HaJa"}],"date_created":"2018-12-11T11:52:02Z","language":[{"iso":"eng"}],"page":"6339 - 6342","file":[{"date_updated":"2020-07-14T12:44:55Z","file_id":"5255","access_level":"open_access","file_name":"IST-2017-840-v1+1_reichhart.pdf","relation":"main_file","checksum":"26da07960e57ac4750b54179197ce57f","creator":"system","date_created":"2018-12-12T10:17:03Z","content_type":"application/pdf","file_size":1268662}],"article_processing_charge":"No","date_published":"2016-05-17T00:00:00Z","doi":"10.1002/anie.201601736","volume":55,"oa":1,"date_updated":"2026-07-08T05:54:25Z","abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"ec_funded":1,"quality_controlled":"1","type":"journal_article","scopus_import":"1","publication":"Angewandte Chemie International Edition","ddc":["571","576"],"corr_author":"1","intvolume":"        55"},{"publist_id":"5928","acknowledgement":"We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140).","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"isi":["000386152800065"],"arxiv":["1607.04406"]},"isi":1,"status":"public","publisher":"American Institute of Physics","article_number":"143507","_id":"1339","oa_version":"Preprint","citation":{"ama":"Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. <i>Applied Physics Letter</i>. 2016;109. doi:<a href=\"https://doi.org/10.1063/1.4964122\">10.1063/1.4964122</a>","apa":"Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. <i>Applied Physics Letter</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4964122\">https://doi.org/10.1063/1.4964122</a>","short":"G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016).","mla":"Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” <i>Applied Physics Letter</i>, vol. 109, 143507, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4964122\">10.1063/1.4964122</a>.","chicago":"Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” <i>Applied Physics Letter</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4964122\">https://doi.org/10.1063/1.4964122</a>.","ieee":"G. Verbiest <i>et al.</i>, “Tunable mechanical coupling between driven microelectromechanical resonators,” <i>Applied Physics Letter</i>, vol. 109. American Institute of Physics, 2016.","ista":"Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507."},"title":"Tunable mechanical coupling between driven microelectromechanical resonators","abstract":[{"lang":"eng","text":"We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n"}],"quality_controlled":"1","scopus_import":"1","type":"journal_article","arxiv":1,"publication":"Applied Physics Letter","intvolume":"       109","article_processing_charge":"No","date_published":"2016-10-04T00:00:00Z","doi":"10.1063/1.4964122","volume":109,"oa":1,"date_updated":"2026-07-08T06:31:59Z","main_file_link":[{"url":"https://arxiv.org/abs/1607.04406","open_access":"1"}],"month":"10","das_tickbox":"1","author":[{"first_name":"Gerard","full_name":"Verbiest, Gerard","last_name":"Verbiest"},{"last_name":"Xu","full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","first_name":"Duo"},{"full_name":"Goldsche, Matthias","last_name":"Goldsche","first_name":"Matthias"},{"first_name":"Timofiy","last_name":"Khodkov","full_name":"Khodkov, Timofiy"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"last_name":"Von Den Driesch","full_name":"Von Den Driesch, Nils","first_name":"Nils"},{"first_name":"Dan","last_name":"Buca","full_name":"Buca, Dan"},{"last_name":"Stampfer","full_name":"Stampfer, Christoph","first_name":"Christoph"}],"date_created":"2018-12-11T11:51:28Z","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"year":"2016"},{"external_id":{"arxiv":["1508.05982"]},"article_number":"1650014","publisher":"World Scientific Publishing","status":"public","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","mathsc":["57M25","57M27"],"OA_place":"repository","title":"The Bar-Natan theory splits","oa_version":"Preprint","_id":"22171","citation":{"ama":"Wigderson Y. The Bar-Natan theory splits. <i>Journal of Knot Theory and Its Ramifications</i>. 2016;25(04). doi:<a href=\"https://doi.org/10.1142/s0218216516500140\">10.1142/s0218216516500140</a>","apa":"Wigderson, Y. (2016). The Bar-Natan theory splits. <i>Journal of Knot Theory and Its Ramifications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0218216516500140\">https://doi.org/10.1142/s0218216516500140</a>","short":"Y. Wigderson, Journal of Knot Theory and Its Ramifications 25 (2016).","mla":"Wigderson, Yuval. “The Bar-Natan Theory Splits.” <i>Journal of Knot Theory and Its Ramifications</i>, vol. 25, no. 04, 1650014, World Scientific Publishing, 2016, doi:<a href=\"https://doi.org/10.1142/s0218216516500140\">10.1142/s0218216516500140</a>.","chicago":"Wigderson, Yuval. “The Bar-Natan Theory Splits.” <i>Journal of Knot Theory and Its Ramifications</i>. World Scientific Publishing, 2016. <a href=\"https://doi.org/10.1142/s0218216516500140\">https://doi.org/10.1142/s0218216516500140</a>.","ieee":"Y. Wigderson, “The Bar-Natan theory splits,” <i>Journal of Knot Theory and Its Ramifications</i>, vol. 25, no. 04. World Scientific Publishing, 2016.","ista":"Wigderson Y. 2016. The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. 25(04), 1650014."},"date_published":"2016-04-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-14T08:48:58Z","oa":1,"volume":25,"doi":"10.1142/s0218216516500140","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"We show that over the binary field [Formula: see text], the Bar-Natan perturbation of Khovanov homology splits as the direct sum of its two reduced theories, which we also prove are isomorphic. This extends Shumakovitch’s analogous result for ordinary Khovanov homology, without the perturbation. "}],"intvolume":"        25","publication":"Journal of Knot Theory and Its Ramifications","arxiv":1,"OA_type":"green","type":"journal_article","scopus_import":"1","extern":"1","year":"2016","publication_identifier":{"issn":["0218-2165"],"eissn":["1793-6527"]},"issue":"04","month":"04","keyword":["Khovanov homology","categorification","Bar-Natan theory","link homology"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1508.05982"}],"date_created":"2026-06-29T10:56:23Z","language":[{"iso":"eng"}],"author":[{"first_name":"Yuval","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","full_name":"Wigderson, Yuval","last_name":"Wigderson"}]},{"article_processing_charge":"No","date_published":"2016-09-01T00:00:00Z","oa":1,"date_updated":"2026-07-14T11:35:58Z","doi":"10.1002/jcd.21522","volume":24,"article_type":"original","abstract":[{"lang":"eng","text":"We use modular symmetric designs to study the existence of Hadamard matrices modulo certain primes. We solve the 7-modular and 11-modular versions of the Hadamard conjecture for all but a finite number of cases. In doing so, we state a conjectural sufficient condition for the existence of a p-modular Hadamard matrix for all but finitely many cases. When 2 is a primitive root of a prime p, we conditionally solve this conjecture and therefore the p-modular version of the Hadamard conjecture for all but finitely many cases when p ≡ 3(mod 4), and prove a weaker result for p ≡ 1 (mod 4). Finally, we look at constraints on the existence of m-modular Hadamard matrices when the size of the matrix is small compared to m."}],"quality_controlled":"1","publication":"Journal of Combinatorial Designs","intvolume":"        24","type":"journal_article","arxiv":1,"scopus_import":"1","OA_type":"green","extern":"1","year":"2016","publication_identifier":{"issn":["1063-8539"],"eissn":["1520-6610"]},"issue":"9","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.0148","open_access":"1"}],"keyword":["modular hadamard matrices","modular symmetric designs"],"month":"09","page":"393-405","author":[{"first_name":"Vivian Zieve","id":"c3bac823-112d-11f0-a3f5-c264f852e697","full_name":"Kuperberg, Vivian Zieve","last_name":"Kuperberg"}],"language":[{"iso":"eng"}],"date_created":"2026-06-29T13:00:27Z","external_id":{"arxiv":["1409.0148"]},"publisher":"Wiley","status":"public","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","OA_place":"repository","title":"Hadamard matrices modulo p and small modular Hadamard matrices","oa_version":"Preprint","_id":"22202","citation":{"mla":"Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” <i>Journal of Combinatorial Designs</i>, vol. 24, no. 9, Wiley, 2016, pp. 393–405, doi:<a href=\"https://doi.org/10.1002/jcd.21522\">10.1002/jcd.21522</a>.","short":"V.Z. Kuperberg, Journal of Combinatorial Designs 24 (2016) 393–405.","ieee":"V. Z. Kuperberg, “Hadamard matrices modulo p and small modular Hadamard matrices,” <i>Journal of Combinatorial Designs</i>, vol. 24, no. 9. Wiley, pp. 393–405, 2016.","chicago":"Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” <i>Journal of Combinatorial Designs</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/jcd.21522\">https://doi.org/10.1002/jcd.21522</a>.","ista":"Kuperberg VZ. 2016. Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. 24(9), 393–405.","ama":"Kuperberg VZ. Hadamard matrices modulo p and small modular Hadamard matrices. <i>Journal of Combinatorial Designs</i>. 2016;24(9):393-405. doi:<a href=\"https://doi.org/10.1002/jcd.21522\">10.1002/jcd.21522</a>","apa":"Kuperberg, V. Z. (2016). Hadamard matrices modulo p and small modular Hadamard matrices. <i>Journal of Combinatorial Designs</i>. Wiley. <a href=\"https://doi.org/10.1002/jcd.21522\">https://doi.org/10.1002/jcd.21522</a>"}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"10","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","publist_id":"5488","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"isi":1,"external_id":{"isi":["000375634100016"]},"publisher":"Academic Press","has_accepted_license":"1","status":"public","oa_version":"Published Version","_id":"1662","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"1399","status":"public"}]},"citation":{"apa":"Edelsbrunner, H., &#38; Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. 2016;287:674-703. doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>","ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” <i>Advances in Mathematics</i>, vol. 287. Academic Press, pp. 674–703, 2016.","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>, vol. 287, Academic Press, 2016, pp. 674–703, doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>.","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703."},"file_date_updated":"2020-07-14T12:45:10Z","title":"Approximation and convergence of the intrinsic volume","quality_controlled":"1","abstract":[{"lang":"eng","text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball."}],"ec_funded":1,"corr_author":"1","intvolume":"       287","publication":"Advances in Mathematics","ddc":["004"],"scopus_import":"1","type":"journal_article","date_published":"2016-01-10T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T10:08:33Z","oa":1,"doi":"10.1016/j.aim.2015.10.004","volume":287,"month":"01","file":[{"content_type":"application/pdf","file_size":248985,"date_created":"2018-12-12T10:12:10Z","checksum":"f8869ec110c35c852ef6a37425374af7","creator":"system","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","relation":"main_file","file_id":"4928","access_level":"open_access","date_updated":"2020-07-14T12:45:10Z"}],"page":"674 - 703","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:53:20Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8379-3768","last_name":"Pausinger","full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"}],"year":"2016","pubrep_id":"774"},{"supervisor":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"month":"12","date_created":"2018-12-11T11:50:16Z","department":[{"_id":"JoBo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","full_name":"Acar, Hande","last_name":"Acar","orcid":"0000-0003-1986-9753"}],"file":[{"file_id":"6814","access_level":"closed","date_updated":"2019-08-13T11:17:50Z","file_name":"PhDThesis_HandeAcar_1230.pdf","relation":"main_file","date_created":"2019-08-13T11:17:50Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","creator":"dernst","file_size":3682711,"content_type":"application/pdf"},{"date_created":"2021-02-22T11:51:13Z","creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_size":3682711,"content_type":"application/pdf","success":1,"access_level":"open_access","file_id":"9184","date_updated":"2021-02-22T11:51:13Z","relation":"main_file","file_name":"2016_Thesis_HandeAcar.pdf"}],"page":"75","year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"abstract":[{"text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments.","lang":"eng"}],"ec_funded":1,"type":"dissertation","corr_author":"1","ddc":["570"],"date_published":"2016-12-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:17:47Z","oa":1,"project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"_id":"1121","oa_version":"Published Version","citation":{"short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria."},"degree_awarded":"PhD","title":"Selective barriers to horizontal gene transfer","OA_place":"publisher","file_date_updated":"2021-02-22T11:51:13Z","publist_id":"6239","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","publication_status":"published","doi_confirm":"1","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"abstract":[{"text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed.","lang":"eng"}],"corr_author":"1","ddc":["004","005","006","532","621"],"type":"dissertation","date_published":"2016-07-15T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-29T11:25:14Z","oa":1,"doi":"10.15479/AT:ISTA:th_640","supervisor":[{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"month":"07","file":[{"date_updated":"2018-12-12T10:13:02Z","file_id":"4982","access_level":"open_access","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","relation":"main_file","creator":"system","date_created":"2018-12-12T10:13:02Z","content_type":"application/pdf","file_size":13869345}],"page":"114","department":[{"_id":"ChWo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:16Z","author":[{"last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten"}],"year":"2016","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"15","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","publist_id":"6238","publication_status":"published","doi_confirm":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","oa_version":"Published Version","_id":"1122","related_material":{"record":[{"id":"5558","status":"public","relation":"other"}]},"citation":{"apa":"Bojsen-Hansen, M. (2016). <i>Tracking, correcting and absorbing water surface waves</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>."},"degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2018-12-12T10:13:02Z","title":"Tracking, correcting and absorbing water surface waves"},{"supervisor":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"month":"02","_id":"1397","oa_version":"None","date_created":"2018-12-11T11:51:47Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"}],"citation":{"short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","mla":"Chmelik, Martin. <i>Algorithms for Partially Observable Markov Decision Processes</i>. Institute of Science and Technology Austria, 2016.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016.","ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","chicago":"Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016.","ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016.","apa":"Chmelik, M. (2016). <i>Algorithms for partially observable markov decision processes</i>. Institute of Science and Technology Austria."},"page":"232","year":"2016","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"title":"Algorithms for partially observable markov decision processes","alternative_title":["ISTA Thesis"],"OA_place":"publisher","publist_id":"5810","abstract":[{"lang":"eng","text":"We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. Based on our theoretical algorithms we also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely. We show that for general integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where  given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs."}],"day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","corr_author":"1","publication_status":"published","date_published":"2016-02-01T00:00:00Z","doi_confirm":"1","article_processing_charge":"No","status":"public","date_updated":"2026-07-29T11:15:18Z","publisher":"Institute of Science and Technology Austria"},{"pubrep_id":"640","year":"2016","title":"Tracking, Correcting and Absorbing Water Surface Waves","file_date_updated":"2020-07-14T12:47:02Z","month":"09","oa_version":"Published Version","_id":"5558","citation":{"ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","short":"M. Bojsen-Hansen, (2016).","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016."},"author":[{"full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ChWo"}],"related_material":{"record":[{"status":"public","id":"1122","relation":"other"}]},"date_created":"2018-12-12T12:31:31Z","datarep_id":"48","file":[{"file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","relation":"main_file","date_updated":"2020-07-14T12:47:02Z","file_id":"5589","access_level":"open_access","content_type":"application/x-bzip2","file_size":55237885,"checksum":"5b1b256ad796fbddb4b7729f5e45e444","creator":"system","date_created":"2018-12-12T13:02:18Z"}],"article_processing_charge":"No","date_published":"2016-09-23T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","has_accepted_license":"1","doi":"10.15479/AT:ISTA:48","publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2026-07-29T11:25:14Z","publist_id":"6238","abstract":[{"lang":"eng","text":"PhD thesis LaTeX source code"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","type":"research_data","ddc":["004"]},{"publication_status":"published","publist_id":"6231","acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","citation":{"ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria."},"_id":"1129","oa_version":"Published Version","title":"Quantitative analysis of haptotactic cell migration","file_date_updated":"2021-02-22T11:43:14Z","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"degree_awarded":"PhD","type":"dissertation","ddc":["570"],"corr_author":"1","abstract":[{"text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale.","lang":"eng"}],"oa":1,"date_updated":"2026-07-29T11:30:22Z","article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","author":[{"full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"department":[{"_id":"MiSi"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:18Z","page":"178","file":[{"date_created":"2019-08-13T10:55:35Z","checksum":"e3cd6b28f9c5cccb8891855565a2dade","creator":"dernst","file_size":32044069,"content_type":"application/pdf","file_id":"6813","access_level":"closed","date_updated":"2019-08-13T10:55:35Z","file_name":"Thesis_JSchwarz_final.pdf","relation":"main_file"},{"access_level":"open_access","file_id":"9181","date_updated":"2021-02-22T11:43:14Z","relation":"main_file","file_name":"2016_Thesis_JSchwarz.pdf","date_created":"2021-02-22T11:43:14Z","creator":"dernst","checksum":"c3dbe219acf87eed2f46d21d5cca00de","file_size":8396717,"success":1,"content_type":"application/pdf"}],"month":"07","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"year":"2016"},{"_id":"1123","oa_version":"Published Version","citation":{"ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","mla":"Mabillard, Isaac. <i>Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture</i>. Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). <i>Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture</i>. Institute of Science and Technology Austria.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016."},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2159"}]},"degree_awarded":"PhD","file_date_updated":"2021-02-22T11:36:34Z","OA_place":"publisher","title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"6237","publication_status":"published","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","month":"08","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"page":"55","file":[{"content_type":"application/pdf","file_size":2227916,"date_created":"2019-08-13T08:45:27Z","creator":"dernst","checksum":"2d140cc924cd1b764544906fc22684ef","relation":"main_file","file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","access_level":"closed","file_id":"6809","date_updated":"2019-08-13T08:45:27Z"},{"success":1,"file_size":2227916,"content_type":"application/pdf","checksum":"2d140cc924cd1b764544906fc22684ef","creator":"dernst","date_created":"2021-02-22T11:36:34Z","file_name":"2016_Mabillard_Thesis.pdf","relation":"main_file","date_updated":"2021-02-22T11:36:34Z","file_id":"9178","access_level":"open_access"}],"author":[{"full_name":"Mabillard, Isaac","last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"UlWa"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:16Z","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems  in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K  can be mapped into Rd  without triple, quadruple, or, more generally, r-fold points  (image points with at least r  distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd  that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint  simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction  for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK  = (r ≥ 1)k  and d  = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign  can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN  to Rd  without r-Tverberg points when r not a prime power  and\r\nN  = (d  + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K  = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle&quot; and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r  + 1 and r  not a prime power, by a reduction1  to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r  not a prime power.     "}],"ddc":["500"],"corr_author":"1","type":"dissertation","article_processing_charge":"No","date_published":"2016-08-01T00:00:00Z","oa":1,"date_updated":"2026-07-29T11:26:07Z"},{"supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"month":"11","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:17Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"page":"127","file":[{"content_type":"application/pdf","file_size":2140062,"creator":"system","date_created":"2018-12-12T10:14:07Z","relation":"main_file","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","date_updated":"2018-12-12T10:14:07Z","access_level":"open_access","file_id":"5056"}],"pubrep_id":"776","year":"2016","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets.","lang":"eng"}],"ec_funded":1,"type":"dissertation","ddc":["006"],"corr_author":"1","article_processing_charge":"No","date_published":"2016-11-01T00:00:00Z","doi":"10.15479/AT:ISTA:TH_776","oa":1,"date_updated":"2026-07-29T11:28:23Z","project":[{"name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7"}],"oa_version":"Published Version","_id":"1126","citation":{"ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>","apa":"Pentina, A. (2016). <i>Theoretical foundations of multi-task lifelong learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>","mla":"Pentina, Anastasia. <i>Theoretical Foundations of Multi-Task Lifelong Learning</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>.","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016."},"degree_awarded":"PhD","title":"Theoretical foundations of multi-task lifelong learning","file_date_updated":"2018-12-12T10:14:07Z","OA_place":"publisher","publist_id":"6234","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","publication_status":"published","doi_confirm":"1","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria"},{"status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","publication_status":"published","publist_id":"6235","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Evolutionary proccesses in variable emvironments","OA_place":"publisher","file_date_updated":"2021-02-22T13:42:47Z","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"2023","status":"public"}]},"citation":{"ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria."},"_id":"1125","oa_version":"Published Version","date_updated":"2026-07-29T11:27:43Z","oa":1,"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","type":"dissertation","corr_author":"1","ddc":["576"],"abstract":[{"lang":"eng","text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model."}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:17Z","language":[{"iso":"eng"}],"author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"file":[{"checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","creator":"dernst","date_created":"2019-08-13T09:01:00Z","file_size":3564901,"content_type":"application/pdf","date_updated":"2019-08-13T09:01:00Z","file_id":"6811","access_level":"closed","file_name":"Novak_thesis.pdf","relation":"main_file"},{"checksum":"30808d2f7ca920e09f63a95cdc49bffd","creator":"dernst","date_created":"2021-02-22T13:42:47Z","file_size":2814384,"content_type":"application/pdf","success":1,"date_updated":"2021-02-22T13:42:47Z","file_id":"9186","access_level":"open_access","file_name":"2016_Novak_Thesis.pdf","relation":"main_file"}],"page":"124","month":"07","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}]},{"title":"Studying the complexities of transcriptional regulation","file_date_updated":"2020-09-21T11:30:40Z","OA_place":"publisher","degree_awarded":"PhD","citation":{"ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016."},"oa_version":"Published Version","_id":"1128","status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","publication_status":"published","publist_id":"6232","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"year":"2016","author":[{"last_name":"Rieckh","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"}],"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:18Z","language":[{"iso":"eng"}],"page":"114","file":[{"relation":"main_file","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","access_level":"closed","file_id":"6815","date_updated":"2019-08-13T11:46:25Z","file_size":2614660,"content_type":"application/pdf","date_created":"2019-08-13T11:46:25Z","creator":"dernst","checksum":"ec453918c3bf8e6f460fd1156ef7b493"},{"date_created":"2020-09-21T11:30:40Z","creator":"dernst","checksum":"51ae398166370d18fd22478b6365c4da","success":1,"content_type":"application/pdf","file_size":6096178,"access_level":"open_access","file_id":"8542","date_updated":"2020-09-21T11:30:40Z","relation":"main_file","file_name":"Thesis_Georg_Rieckh.pdf"}],"supervisor":[{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"month":"08","oa":1,"date_updated":"2026-07-29T11:29:22Z","article_processing_charge":"No","date_published":"2016-08-01T00:00:00Z","type":"dissertation","ddc":["570"],"corr_author":"1","abstract":[{"text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems.","lang":"eng"}]},{"citation":{"mla":"Morri, Maurizio. <i>Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors</i>. Institute of Science and Technology Austria, 2016.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria."},"_id":"1124","oa_version":"Published Version","OA_place":"publisher","file_date_updated":"2021-02-22T11:42:06Z","title":"Optical functionalization of human class A orphan G-protein coupled receptors","degree_awarded":"PhD","publication_status":"published","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"6236","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","doi_confirm":"1","file":[{"relation":"main_file","file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","date_updated":"2019-08-13T10:50:00Z","access_level":"closed","file_id":"6812","file_size":4785167,"content_type":"application/pdf","creator":"dernst","checksum":"b439803ac0827cdddd56562a54e3b53b","date_created":"2019-08-13T10:50:00Z"},{"date_updated":"2021-02-22T11:42:06Z","file_id":"9180","access_level":"open_access","file_name":"2016_MORRI_Thesis.pdf","relation":"main_file","checksum":"dd4136247fe472e7d47880ec68ac8de0","creator":"dernst","date_created":"2021-02-22T11:42:06Z","content_type":"application/pdf","file_size":4495669,"success":1}],"page":"129","department":[{"_id":"HaJa"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:17Z","language":[{"iso":"eng"}],"author":[{"full_name":"Morri, Maurizio","last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016","corr_author":"1","ddc":["570"],"type":"dissertation","date_updated":"2026-07-29T11:26:59Z","oa":1,"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No"},{"date_created":"2018-12-11T11:51:59Z","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"author":[{"full_name":"Mishra, Rajiv Kumar","last_name":"Mishra","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kim","full_name":"Kim, Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","first_name":"Sooyun"},{"full_name":"Guzmán, José","last_name":"Guzmán","orcid":"0000-0003-2209-5242","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804"}],"file":[{"content_type":"application/pdf","file_size":4510512,"checksum":"7e84d0392348c874d473b62f1042de22","creator":"system","date_created":"2018-12-12T10:18:33Z","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_id":"5355","access_level":"open_access"}],"month":"05","pubrep_id":"582","year":"2016","type":"journal_article","scopus_import":"1","corr_author":"1","intvolume":"         7","publication":"Nature Communications","ddc":["570"],"quality_controlled":"1","abstract":[{"text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.","lang":"eng"}],"ec_funded":1,"volume":7,"doi":"10.1038/ncomms11552","date_updated":"2026-07-29T11:31:52Z","oa":1,"date_published":"2016-05-13T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1396"}]},"citation":{"ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>."},"project":[{"call_identifier":"FWF","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"1432","oa_version":"Published Version","title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","file_date_updated":"2020-07-14T12:44:53Z","publication_status":"published","publist_id":"5766","day":"13","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","has_accepted_license":"1","status":"public","article_number":"11552","publisher":"Nature Publishing Group","external_id":{"isi":["000375938200001"]},"isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","doi_confirm":"1","publication_status":"published","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"5811","OA_place":"publisher","file_date_updated":"2021-02-22T11:48:44Z","title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"1432","relation":"part_of_dissertation"}]},"citation":{"apa":"Mishra, R. K. (2016). <i>Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus</i>. Institute of Science and Technology Austria.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016.","ista":"Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria.","ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016.","mla":"Mishra, Rajiv Kumar. <i>Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus</i>. Institute of Science and Technology Austria, 2016.","short":"R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016."},"_id":"1396","oa_version":"Published Version","date_updated":"2026-07-29T11:31:52Z","oa":1,"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","ddc":["570"],"type":"dissertation","abstract":[{"text":"CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2016","file":[{"date_updated":"2020-07-14T12:44:48Z","file_id":"6782","access_level":"closed","file_name":"Thesis_Mishra_Rajiv (Final).pdf","relation":"main_file","checksum":"5a010a838faf040f7064f3cfb802f743","creator":"dernst","date_created":"2019-08-09T12:14:46Z","content_type":"application/pdf","file_size":2407572},{"date_updated":"2021-02-22T11:48:44Z","access_level":"open_access","file_id":"9183","relation":"main_file","file_name":"2016_RajivMishra_Thesis.pdf","creator":"dernst","checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","date_created":"2021-02-22T11:48:44Z","content_type":"application/pdf","success":1,"file_size":2407572}],"page":"83","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:46Z","author":[{"first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar","last_name":"Mishra"}],"month":"03","supervisor":[{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}]}]