[{"abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","related_material":{"record":[{"relation":"used_in_publication","id":"1322","status":"public"}]},"department":[{"_id":"KrCh"}],"date_updated":"2025-09-22T08:27:00Z","type":"research_data_reference","date_created":"2021-08-10T08:42:00Z","author":[{"first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"full_name":"Hagel, Kristin","first_name":"Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}],"doi":"10.1371/journal.pone.0163867.s008","month":"10","title":"Experimental game instructions","day":"04","_id":"9867","citation":{"mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016."},"year":"2016","article_processing_charge":"No","status":"public"},{"date_updated":"2025-09-22T08:27:00Z","department":[{"_id":"KrCh"}],"author":[{"last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"first_name":"Kristin","last_name":"Hagel","full_name":"Hagel, Kristin"},{"first_name":"Manfred","last_name":"Milinski","full_name":"Milinski, Manfred"}],"date_created":"2021-08-10T08:45:00Z","type":"research_data_reference","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The raw data file containing the experimental decisions of all our study subjects."}],"related_material":{"record":[{"status":"public","id":"1322","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","article_processing_charge":"No","status":"public","title":"Experimental data","month":"10","doi":"10.1371/journal.pone.0163867.s009","date_published":"2016-10-04T00:00:00Z","_id":"9868","citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>."},"year":"2016","day":"04"},{"author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"date_created":"2021-08-10T08:53:48Z","type":"research_data_reference","date_updated":"2025-09-22T08:46:14Z","department":[{"_id":"GaTk"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"status":"public","article_processing_charge":"No","year":"2016","_id":"9869","citation":{"short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>"},"day":"27","title":"Error bound on an estimator of position","doi":"10.1371/journal.pone.0163628.s001","month":"09","date_published":"2016-09-27T00:00:00Z"},{"article_processing_charge":"No","status":"public","month":"09","doi":"10.1371/journal.pone.0163628.s002","title":"Computation of positional information in an Ising model","date_published":"2016-09-27T00:00:00Z","day":"27","citation":{"apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"_id":"9870","year":"2016","date_updated":"2025-09-22T08:46:14Z","department":[{"_id":"GaTk"}],"date_created":"2021-08-10T09:23:45Z","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","oa_version":"Published Version","abstract":[{"text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"abstract":[{"lang":"eng","text":"The positional information in a discrete morphogen field with Gaussian noise is computed."}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"department":[{"_id":"GaTk"}],"date_updated":"2025-09-22T08:46:14Z","type":"research_data_reference","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"date_created":"2021-08-10T09:27:35Z","title":"Computation of positional information in a discrete morphogen field","doi":"10.1371/journal.pone.0163628.s003","month":"09","_id":"9871","citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. 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Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 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Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016."},"day":"19","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","doi":"10.1371/journal.pgen.1005974.s015","month":"04","status":"public","article_processing_charge":"No"},{"page":"233-245","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"02","_id":"19990","year":"2016","citation":{"ieee":"H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–245.","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–45, doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>.","ama":"Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Neuromethods. Springer Nature; 2016:233-245. doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>","apa":"Harada, H., &#38; Shigemoto, R. (2016). High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (pp. 233–245). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 233–45. Neuromethods. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>.","ista":"Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. , 233–245."},"date_published":"2016-02-02T00:00:00Z","doi":"10.1007/978-1-4939-3064-7_17","month":"02","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","publication_status":"published","type":"book_chapter","date_created":"2025-07-10T13:56:06Z","series_title":"Neuromethods","quality_controlled":"1","author":[{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto"}],"publication_identifier":{"eisbn":["9781493930647"],"isbn":["9781493930630"],"eissn":["1940-6045"],"issn":["0893-2336"]},"department":[{"_id":"RySh"}],"corr_author":"1","date_updated":"2026-04-07T08:32:03Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Springer Nature","OA_type":"closed access","publication":"Receptor and Ion Channel Detection in the Brain","abstract":[{"text":"Visualizing molecular localization at high resolution contributes to understanding of their functions and roles in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study high-resolution two-dimensional distribution of transmembrane proteins and their tightly associated proteins on platinum-carbon replica. During treatment with SDS, unfixed proteins and intracellular organelle are dissolved and integral membrane proteins captured and stabilized by carbon and platinum deposition are denatured, retaining most of their antigenicity, and exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure of these antigens on the surface of replica facilitates the accessibility of antibodies and therefore provides higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples and an additional procedure for fluorescence-guided electron microscopy for replica immunolabeling.","lang":"eng"}],"oa_version":"None"},{"date_updated":"2026-04-08T07:27:13Z","author":[{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"full_name":"Kloeffel, Christoph","last_name":"Kloeffel","first_name":"Christoph"},{"full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636","last_name":"Vukusic","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rossell","first_name":"Marta","full_name":"Rossell, Marta"},{"full_name":"Sessi, Violetta","first_name":"Violetta","last_name":"Sessi"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip"},{"full_name":"Kirchschlager, Raimund","last_name":"Kirchschlager","first_name":"Raimund"},{"id":"33662F76-F248-11E8-B48F-1D18A9856A87","last_name":"Lausecker","first_name":"Elisabeth","full_name":"Lausecker, Elisabeth"},{"full_name":"Truhlar, Alisha","first_name":"Alisha","last_name":"Truhlar","id":"49CBC780-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Glaser","full_name":"Glaser, Martin"},{"full_name":"Rastelli, Armando","last_name":"Rastelli","first_name":"Armando"},{"full_name":"Fuhrer, Andreas","last_name":"Fuhrer","first_name":"Andreas"},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"date_created":"2018-12-11T11:51:24Z","project":[{"grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","abstract":[{"text":"Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples.","lang":"eng"}],"volume":16,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000387625000025"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"Heavy-hole states in germanium hut wires","scopus_import":"1","month":"09","date_published":"2016-09-22T00:00:00Z","_id":"1328","pubrep_id":"664","year":"2016","intvolume":"        16","file":[{"file_size":535121,"content_type":"application/pdf","file_id":"5053","access_level":"open_access","checksum":"b63feece90d7b620ece49ca632e34ff3","creator":"system","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-664-v1+1_acs.nanolett.6b02715.pdf","date_created":"2018-12-12T10:14:04Z","relation":"main_file"}],"corr_author":"1","department":[{"_id":"GeKa"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","publication":"Nano Letters","ddc":["539"],"has_accepted_license":"1","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"relation":"dissertation_contains","id":"7996","status":"public"}]},"publisher":"American Chemical Society","file_date_updated":"2020-07-14T12:44:44Z","page":"6879 - 6885","acknowledgement":"The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. ","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"11","doi":"10.1021/acs.nanolett.6b02715","citation":{"ieee":"H. Watzinger <i>et al.</i>, “Heavy-hole states in germanium hut wires,” <i>Nano Letters</i>, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016.","short":"H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.","ama":"Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. 2016;16(11):6879-6885. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>","apa":"Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>","ista":"Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.","chicago":"Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>.","mla":"Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>."},"isi":1,"day":"22","publist_id":"5941"},{"abstract":[{"text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.","lang":"eng"}],"oa_version":"Published Version","external_id":{"isi":["000377899800001"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":7,"date_updated":"2026-04-08T13:54:44Z","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"full_name":"Kuenen, Sabine","last_name":"Kuenen","first_name":"Sabine"},{"full_name":"Mylle, Evelien","first_name":"Evelien","last_name":"Mylle"},{"full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","last_name":"Keech","full_name":"Keech, Olivier"},{"last_name":"Viotti","first_name":"Corrado","full_name":"Viotti, Corrado"},{"full_name":"Swerts, Jef","first_name":"Jef","last_name":"Swerts"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Ortiz Morea, Fausto","first_name":"Fausto","last_name":"Ortiz Morea"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"full_name":"Delang, Simon","first_name":"Simon","last_name":"Delang"},{"first_name":"Stefan","last_name":"Scholl","full_name":"Scholl, Stefan"},{"full_name":"Zarza, Xavier","last_name":"Zarza","first_name":"Xavier"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"first_name":"Jiorgos","last_name":"Kourelis","full_name":"Kourelis, Jiorgos"},{"first_name":"Jaroslaw","last_name":"Kasprowicz","full_name":"Kasprowicz, Jaroslaw"},{"last_name":"Nguyen","first_name":"Le","full_name":"Nguyen, Le"},{"full_name":"Drozdzecki, Andrzej","first_name":"Andrzej","last_name":"Drozdzecki"},{"full_name":"Van Houtte, Isabelle","first_name":"Isabelle","last_name":"Van Houtte"},{"last_name":"Szatmári","first_name":"Anna","full_name":"Szatmári, Anna"},{"last_name":"Majda","first_name":"Mateusz","full_name":"Majda, Mateusz"},{"first_name":"Gary","last_name":"Baisa","full_name":"Baisa, Gary"},{"full_name":"Bednarek, Sebastian","first_name":"Sebastian","last_name":"Bednarek"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Audenaert","first_name":"Dominique","full_name":"Audenaert, Dominique"},{"last_name":"Testerink","first_name":"Christa","full_name":"Testerink, Christa"},{"full_name":"Munnik, Teun","first_name":"Teun","last_name":"Munnik"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"last_name":"Schumacher","first_name":"Karin","full_name":"Schumacher, Karin"},{"full_name":"Winne, Johan","first_name":"Johan","last_name":"Winne"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Verstreken","first_name":"Patrik","full_name":"Verstreken, Patrik"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"date_created":"2018-12-11T11:51:30Z","date_published":"2016-06-08T00:00:00Z","title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","month":"06","scopus_import":"1","intvolume":"         7","_id":"1346","pubrep_id":"653","year":"2016","language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public","ddc":["570"],"publication":"Nature Communications","publisher":"Nature Publishing Group","related_material":{"record":[{"id":"7172","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","department":[{"_id":"JiFr"}],"file":[{"file_id":"5369","file_size":3532505,"content_type":"application/pdf","date_created":"2018-12-12T10:18:47Z","relation":"main_file","access_level":"open_access","creator":"system","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","article_number":"11710","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","doi":"10.1038/ncomms11710","citation":{"mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>, vol. 7, 11710, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>.","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>.","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","ieee":"W. Dejonghe <i>et al.</i>, “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"isi":1,"publist_id":"5906","day":"08","file_date_updated":"2020-07-14T12:44:45Z"},{"type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"corr_author":"1","file":[{"relation":"main_file","date_created":"2018-12-12T10:12:01Z","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","access_level":"open_access","creator":"system","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_id":"4919","content_type":"application/pdf","file_size":861805},{"file_id":"4920","content_type":"application/pdf","file_size":1084703,"relation":"main_file","date_created":"2018-12-12T10:12:02Z","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","creator":"system","checksum":"164864a1a675f3ad80e9917c27aba07f","access_level":"open_access"}],"publisher":"Nature Publishing Group","related_material":{"record":[{"relation":"dissertation_contains","id":"6071","status":"public"}]},"has_accepted_license":"1","ddc":["576"],"publication":"Nature Communications","file_date_updated":"2020-07-14T12:44:46Z","citation":{"mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016)."},"day":"04","isi":1,"publist_id":"5887","article_number":"12307","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/ncomms12307","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_created":"2018-12-11T11:51:34Z","date_updated":"2026-04-08T13:54:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000380858400001"]},"volume":7,"oa":1,"abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"         7","year":"2016","_id":"1358","pubrep_id":"627","date_published":"2016-08-04T00:00:00Z","title":"Intrinsic limits to gene regulation by global crosstalk","scopus_import":"1","month":"08"},{"year":"2016","_id":"1096","intvolume":"        37","title":"Actin rings of power","scopus_import":"1","month":"06","date_published":"2016-06-20T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":37,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000378204200005"]},"oa_version":"None","author":[{"last_name":"Schwayer","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"first_name":"Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","last_name":"Kardos","full_name":"Kardos, Roland"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2018-12-11T11:50:07Z","date_updated":"2026-04-08T13:55:28Z","citation":{"ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” <i>Developmental Cell</i>, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” <i>Developmental Cell</i>, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. <i>Developmental Cell</i>. 2016;37(6):493-506. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., &#38; Heisenberg, C.-P. J. (2016). Actin rings of power. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>."},"publist_id":"6279","isi":1,"day":"20","doi":"10.1016/j.devcel.2016.05.024","issue":"6","page":"493 - 506","related_material":{"record":[{"status":"public","id":"7186","relation":"part_of_dissertation"}]},"publisher":"Cell Press","publication":"Developmental Cell","quality_controlled":"1","type":"journal_article","publication_status":"published","department":[{"_id":"CaHe"}]},{"citation":{"mla":"Abusalah, Hamza M., et al. <i>Offline Witness Encryption</i>. Vol. 9696, Springer, 2016, pp. 285–303, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303."},"isi":1,"publist_id":"6105","day":"09","acknowledgement":"Research  supported  by  the  European  Research  Council,  ERC  starting  grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","doi":"10.1007/978-3-319-39555-5_16","conference":{"start_date":"2016-06-19","location":"Guildford, UK","end_date":"2016-06-22","name":"ACNS: Applied Cryptography and Network Security"},"page":"285 - 303","file_date_updated":"2020-07-14T12:44:39Z","publisher":"Springer","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"83"}]},"has_accepted_license":"1","ddc":["005","600"],"type":"conference","publication_status":"published","quality_controlled":"1","department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"file":[{"file_size":515000,"content_type":"application/pdf","file_id":"5273","file_name":"IST-2017-765-v1+1_838.pdf","date_updated":"2020-07-14T12:44:39Z","checksum":"34fa9ce681da845a1ba945ba3dc57867","creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:20Z"}],"intvolume":"      9696","_id":"1229","pubrep_id":"765","year":"2016","date_published":"2016-06-09T00:00:00Z","title":"Offline witness encryption","scopus_import":"1","month":"06","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000386324500016"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":9696,"abstract":[{"lang":"eng","text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card."}],"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"author":[{"full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2018-12-11T11:50:50Z","date_updated":"2026-04-08T14:10:21Z"},{"date_updated":"2026-04-08T14:10:21Z","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M","full_name":"Abusalah, Hamza M"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2018-12-11T11:50:52Z","abstract":[{"text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key.","lang":"eng"}],"oa_version":"Submitted Version","external_id":{"isi":["000374102500024"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":9610,"oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public","date_published":"2016-02-02T00:00:00Z","title":"Constrained PRFs for unbounded inputs","month":"02","scopus_import":"1","intvolume":"      9610","_id":"1236","year":"2016","pubrep_id":"764","department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"file":[{"relation":"main_file","date_created":"2018-12-12T10:08:05Z","date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2017-764-v1+1_279.pdf","access_level":"open_access","creator":"system","checksum":"3851cee49933ae13b1272e516f213e13","file_id":"4664","file_size":495176,"content_type":"application/pdf"}],"type":"conference","publication_status":"published","quality_controlled":"1","ddc":["005","600"],"publisher":"Springer","related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:41Z","page":"413 - 428","conference":{"start_date":"2016-02-29","location":"San Francisco, CA, USA","name":"CT-RSA: Topics in Cryptology","end_date":"2016-03-04"},"acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","doi":"10.1007/978-3-319-29485-8_24","citation":{"short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>."},"day":"02","publist_id":"6097","isi":1},{"intvolume":"      9696","_id":"1235","year":"2016","date_published":"2016-01-01T00:00:00Z","scopus_import":"1","month":"01","title":"Constrained PRFs for unbounded inputs with short keys","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000386324500024"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":9696,"oa":1,"abstract":[{"text":"A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation.","lang":"eng"}],"oa_version":"Submitted Version","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2018-12-11T11:50:52Z","author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M","full_name":"Abusalah, Hamza M"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"}],"date_updated":"2026-04-08T14:10:21Z","day":"01","isi":1,"publist_id":"6098","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/279.pdf"}],"citation":{"mla":"Abusalah, Hamza M., and Georg Fuchsbauer. <i>Constrained PRFs for Unbounded Inputs with Short Keys</i>. Vol. 9696, Springer, 2016, pp. 445–63, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>.","ama":"Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short keys. In: Vol 9696. Springer; 2016:445-463. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">10.1007/978-3-319-39555-5_24</a>","apa":"Abusalah, H. M., &#38; Fuchsbauer, G. (2016). Constrained PRFs for unbounded inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>","ista":"Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 445–463.","chicago":"Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded Inputs with Short Keys,” 9696:445–63. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_24\">https://doi.org/10.1007/978-3-319-39555-5_24</a>.","ieee":"H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs with short keys,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 445–463.","short":"H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463."},"doi":"10.1007/978-3-319-39555-5_24","acknowledgement":"H. Abusalah—Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","page":"445 - 463","conference":{"end_date":"2016-06-22","name":"ACNS: Applied Cryptography and Network Security","location":"Guildford, UK","start_date":"2016-06-19"},"publisher":"Springer","related_material":{"record":[{"status":"public","id":"83","relation":"dissertation_contains"}]},"publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"KrPi"}],"alternative_title":["LNCS"]},{"quality_controlled":"1","publication_status":"published","type":"journal_article","corr_author":"1","file":[{"file_id":"5255","content_type":"application/pdf","file_size":1268662,"relation":"main_file","date_created":"2018-12-12T10:17:03Z","date_updated":"2020-07-14T12:44:55Z","file_name":"IST-2017-840-v1+1_reichhart.pdf","checksum":"26da07960e57ac4750b54179197ce57f","creator":"system","access_level":"open_access"}],"department":[{"_id":"HaJa"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"}]},"has_accepted_license":"1","publisher":"Wiley","ddc":["571","576"],"publication":"Angewandte Chemie - International Edition","page":"6339 - 6342","file_date_updated":"2020-07-14T12:44:55Z","publist_id":"5755","isi":1,"day":"17","citation":{"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.","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>.","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>","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>","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.","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>."},"issue":"21","doi":"10.1002/anie.201601736","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).","date_created":"2018-12-11T11:52:02Z","author":[{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto"},{"first_name":"Alexandra-Madelaine","last_name":"Tichy","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tichy, Alexandra-Madelaine"},{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"date_updated":"2026-04-08T14:11:53Z","volume":55,"oa":1,"external_id":{"isi":["000377918400039"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","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"}],"status":"public","ec_funded":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"1441","year":"2016","pubrep_id":"840","intvolume":"        55","scopus_import":"1","month":"05","title":"A phytochrome sensory domain permits receptor activation by red light","date_published":"2016-05-17T00:00:00Z"},{"file_date_updated":"2020-07-14T12:44:46Z","conference":{"start_date":"2016-07-24","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","end_date":"2016-07-28"},"issue":"4","doi":"10.1145/2897824.2925902","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"104","publist_id":"5880","day":"01","isi":1,"citation":{"short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","mla":"Hahn, David, and Chris Wojtan. <i>Fast Approximations for Boundary Element Based Brittle Fracture Simulation</i>. Vol. 35, no. 4, 104, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>.","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>.","ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>","apa":"Hahn, D., &#38; Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>"},"corr_author":"1","file":[{"access_level":"open_access","creator":"system","checksum":"943712d9c9dc8bb5048d4adc561d7d38","file_name":"IST-2016-632-v1+2_a104-hahn.pdf","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:15:04Z","relation":"main_file","content_type":"application/pdf","file_size":12453704,"file_id":"5121"}],"alternative_title":["ACM Transactions on Graphics"],"department":[{"_id":"ChWo"}],"quality_controlled":"1","publication_status":"published","type":"conference","ddc":["000"],"related_material":{"record":[{"id":"839","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","publisher":"ACM","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","ec_funded":1,"month":"07","scopus_import":"1","title":"Fast approximations for boundary element based brittle fracture simulation","date_published":"2016-07-01T00:00:00Z","_id":"1362","pubrep_id":"632","year":"2016","intvolume":"        35","date_updated":"2026-04-08T14:20:15Z","date_created":"2018-12-11T11:51:35Z","author":[{"first_name":"David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches."}],"volume":35,"oa":1,"external_id":{"isi":["000380112400074"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"202","status":"public"}]},"publisher":"Cell Press","publication":"Current Biology","quality_controlled":"1","publication_status":"published","type":"journal_article","department":[{"_id":"CaGu"}],"publist_id":"6087","day":"08","isi":1,"citation":{"mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>.","chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>.","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. 2016;26(3):404-409. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">10.1016/j.cub.2015.12.041</a>","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., &#38; Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.12.041\">https://doi.org/10.1016/j.cub.2015.12.041</a>","short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","ieee":"M. Pleska <i>et al.</i>, “Bacterial autoimmunity due to a restriction-modification system,” <i>Current Biology</i>, vol. 26, no. 3. Cell Press, pp. 404–409, 2016."},"doi":"10.1016/j.cub.2015.12.041","issue":"3","acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","page":"404 - 409","volume":26,"external_id":{"isi":["000369502900034"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","abstract":[{"text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.","lang":"eng"}],"date_created":"2018-12-11T11:50:54Z","author":[{"full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qian, Long","last_name":"Qian","first_name":"Long"},{"full_name":"Okura, Reiko","last_name":"Okura","first_name":"Reiko"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"full_name":"Wakamoto, Yuichi","last_name":"Wakamoto","first_name":"Yuichi"},{"first_name":"Edo","last_name":"Kussell","full_name":"Kussell, Edo"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210"}],"date_updated":"2026-04-08T14:19:43Z","year":"2016","_id":"1243","intvolume":"        26","scopus_import":"1","month":"02","title":"Bacterial autoimmunity due to a restriction-modification system","date_published":"2016-02-08T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}]},{"volume":57,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:49:59Z","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-04-08T14:22:16Z","_id":"1071","year":"2016","pubrep_id":"777","intvolume":"        57","title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","scopus_import":"1","month":"08","date_published":"2016-08-01T00:00:00Z","ec_funded":1,"status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"id":"821","status":"public","relation":"dissertation_contains"}]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["004","006"],"quality_controlled":"1","type":"conference","publication_status":"published","file":[{"file_size":579225,"content_type":"application/pdf","file_id":"5084","date_updated":"2018-12-12T10:14:31Z","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:14:31Z"}],"alternative_title":["LIPIcs"],"department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"day":"01","publist_id":"6312","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","doi":"10.4230/LIPIcs.ESA.2016.28","article_number":"28","conference":{"location":"Aarhus, Denmark","name":"ESA: European Symposium on Algorithms","end_date":"2016-08-24","start_date":"2016-08-22"},"file_date_updated":"2018-12-12T10:14:31Z"},{"publist_id":"5810","day":"01","year":"2016","_id":"1397","citation":{"ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016.","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.","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.","chicago":"Chmelik, Martin. “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."},"degree_awarded":"PhD","month":"02","title":"Algorithms for partially observable markov decision processes","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_published":"2016-02-01T00:00:00Z","status":"public","page":"232","article_processing_charge":"No","language":[{"iso":"eng"}],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","oa_version":"None","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:51:47Z","author":[{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"}],"publication_status":"published","type":"dissertation","alternative_title":["ISTA Thesis"],"corr_author":"1","date_updated":"2026-04-08T14:23:19Z","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"KrCh"}]},{"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"}],"date_created":"2018-12-11T11:50:18Z","date_updated":"2026-04-08T14:28:53Z","publication_identifier":{"issn":["2663-337X"]},"_id":"1129","year":"2016","degree_awarded":"PhD","title":"Quantitative analysis of haptotactic cell migration","month":"07","date_published":"2016-07-01T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","ddc":["570"],"type":"dissertation","publication_status":"published","alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"date_updated":"2019-08-13T10:55:35Z","file_name":"Thesis_JSchwarz_final.pdf","access_level":"closed","checksum":"e3cd6b28f9c5cccb8891855565a2dade","creator":"dernst","relation":"main_file","date_created":"2019-08-13T10:55:35Z","content_type":"application/pdf","file_size":32044069,"file_id":"6813"},{"file_id":"9181","success":1,"file_size":8396717,"content_type":"application/pdf","relation":"main_file","date_created":"2021-02-22T11:43:14Z","file_name":"2016_Thesis_JSchwarz.pdf","date_updated":"2021-02-22T11:43:14Z","creator":"dernst","checksum":"c3dbe219acf87eed2f46d21d5cca00de","access_level":"open_access"}],"department":[{"_id":"MiSi"}],"citation":{"mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 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."},"publist_id":"6231","day":"01","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","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"}],"page":"178","file_date_updated":"2021-02-22T11:43:14Z"}]