[{"year":"2017","conference":{"start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Aalborg, Denmark"},"date_updated":"2021-01-12T08:02:35Z","oa":1,"month":"11","intvolume":"        83","date_published":"2017-11-01T00:00:00Z","alternative_title":["LIPIcs"],"article_number":"55","oa_version":"Published Version","main_file_link":[{"url":"https://arxiv.org/abs/1506.02434","open_access":"1"}],"doi":"10.4230/LIPIcs.MFCS.2017.55","publication":"Leibniz International Proceedings in Informatics","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:08Z","ddc":["004"],"day":"01","status":"public","volume":83,"language":[{"iso":"eng"}],"pubrep_id":"922","publist_id":"7261","department":[{"_id":"KrCh"}],"file":[{"date_created":"2018-12-12T10:09:29Z","date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","checksum":"7101facb56ade363205c695d72dbd173","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4753","file_size":549967,"creator":"system"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Hansen, Kristofer","last_name":"Hansen","first_name":"Kristofer"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Strategy complexity of concurrent safety games","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","_id":"553","quality_controlled":"1","publication_identifier":{"isbn":["978-395977046-0"]},"citation":{"mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” <i>Leibniz International Proceedings in Informatics</i>, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">10.4230/LIPIcs.MFCS.2017.55</a>.","apa":"Chatterjee, K., Hansen, K., &#38; Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">https://doi.org/10.4230/LIPIcs.MFCS.2017.55</a>","chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">https://doi.org/10.4230/LIPIcs.MFCS.2017.55</a>.","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">10.4230/LIPIcs.MFCS.2017.55</a>","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in <i>Leibniz International Proceedings in Informatics</i>, Aalborg, Denmark, 2017, vol. 83.","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55."},"type":"conference","file_date_updated":"2020-07-14T12:47:00Z","scopus_import":1,"abstract":[{"lang":"eng","text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. "}]},{"article_processing_charge":"No","department":[{"_id":"KrCh"}],"year":"2017","date_published":"2017-01-02T00:00:00Z","datarep_id":"51","has_accepted_license":"1","month":"01","publisher":"Institute of Science and Technology Austria","keyword":["natural selection"],"date_updated":"2024-02-21T13:48:42Z","title":"Strong amplifiers of natural selection","author":[{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak ","full_name":"Nowak , Martin"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5644","content_type":"video/mp4","creator":"system","file_size":32987015,"checksum":"b427dd46a30096a1911b245640c47af8","access_level":"open_access","relation":"main_file","file_name":"IST-2017-51-v1+2_illustration.mp4","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:05:18Z"}],"project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:51","related_material":{"record":[{"id":"5452","relation":"research_paper","status":"public"},{"relation":"research_paper","status":"public","id":"5751"}]},"ec_funded":1,"oa_version":"Published Version","citation":{"mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak , M. (2017). Strong amplifiers of natural selection. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak . “Strong Amplifiers of Natural Selection.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. Strong amplifiers of natural selection. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak , (2017).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak , “Strong amplifiers of natural selection.” Institute of Science and Technology Austria, 2017.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. 2017. Strong amplifiers of natural selection, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>."},"abstract":[{"text":"Strong amplifiers of natural selection","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","_id":"5559","date_created":"2018-12-12T12:31:32Z","ddc":["519"],"status":"public","day":"02"},{"doi":"10.15479/AT:ISTA:53","related_material":{"record":[{"id":"665","relation":"research_paper","status":"public"}]},"oa_version":"Published Version","citation":{"short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>","mla":"Bergmiller, Tobias, et al. <i>Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>."},"file_date_updated":"2020-07-14T12:47:03Z","type":"research_data","abstract":[{"lang":"eng","text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication."}],"_id":"5560","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["571"],"date_created":"2018-12-12T12:31:32Z","day":"10","status":"public","article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"year":"2017","month":"03","has_accepted_license":"1","date_published":"2017-03-10T00:00:00Z","datarep_id":"53","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:49:00Z","keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"file":[{"access_level":"open_access","relation":"main_file","checksum":"d77859af757ac8025c50c7b12b52eaf3","creator":"system","file_size":6773204,"file_id":"5603","content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:38Z","file_name":"IST-2017-53-v1+1_Data_MDE.zip"}],"oa":1,"author":[{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna M","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","orcid":"0000-0003-2912-6769","full_name":"Andersson, Anna M"},{"full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"VlKo"}],"article_processing_charge":"No","year":"2017","publisher":"Institute of Science and Technology Austria","acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","has_accepted_license":"1","month":"02","date_published":"2017-02-13T00:00:00Z","datarep_id":"57","file":[{"file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:54Z","content_type":"application/zip","file_id":"5614","creator":"system","file_size":327042819,"checksum":"3dc3e1306a66028a34181ebef2923139","access_level":"open_access","relation":"main_file"}],"oa":1,"title":"Graph matching problems for annotating C. Elegans","author":[{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"first_name":"Florian","last_name":"Jug","full_name":"Jug, Florian"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"},{"full_name":"Meyers, Gene","first_name":"Gene","last_name":"Meyers"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:46:31Z","keyword":["graph matching","feature matching","QAP","MAP-inference"],"doi":"10.15479/AT:ISTA:57","oa_version":"Published Version","type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. ","lang":"eng"}],"citation":{"chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:57\">https://doi.org/10.15479/AT:ISTA:57</a>.","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>","ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>.","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017).","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","mla":"Kainmueller, Dagmar, et al. <i>Graph Matching Problems for Annotating C. Elegans</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>.","apa":"Kainmueller, D., Jug, F., Rother, C., &#38; Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:57\">https://doi.org/10.15479/AT:ISTA:57</a>"},"day":"13","status":"public","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5561","date_created":"2018-12-12T12:31:32Z","ddc":["000"]},{"keyword":["multi-electrode recording","retinal ganglion cells"],"date_updated":"2024-02-21T13:46:14Z","oa":1,"title":"Multi-electrode array recording from salamander retinal ganglion cells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"file":[{"creator":"system","file_size":1336936,"content_type":"application/octet-stream","file_id":"5622","relation":"main_file","checksum":"e620eff260646f57b479a69492c8b765","access_level":"open_access","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:03:04Z"},{"date_created":"2018-12-12T13:03:05Z","date_updated":"2020-07-14T12:47:03Z","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","relation":"main_file","access_level":"open_access","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","creator":"system","file_size":1897543,"file_id":"5623","content_type":"application/zip"}],"date_published":"2017-02-27T00:00:00Z","datarep_id":"61","has_accepted_license":"1","month":"02","publisher":"Institute of Science and Technology Austria","year":"2017","article_processing_charge":"No","department":[{"_id":"GaTk"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5562","date_created":"2018-12-12T12:31:33Z","ddc":["570"],"day":"27","status":"public","citation":{"mla":"Marre, Olivier, et al. <i>Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>.","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., &#38; Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:61\">https://doi.org/10.15479/AT:ISTA:61</a>","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:61\">https://doi.org/10.15479/AT:ISTA:61</a>.","ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>"},"abstract":[{"text":"This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.","lang":"eng"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"2257"}]},"oa_version":"Published Version","doi":"10.15479/AT:ISTA:61"},{"doi":"10.15479/AT:ISTA:64","oa_version":"Published Version","abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","citation":{"chicago":"Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:64\">https://doi.org/10.15479/AT:ISTA:64</a>.","ista":"Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:64\">10.15479/AT:ISTA:64</a>.","short":"M. Lukacisin, (2017).","ieee":"M. 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Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. ","lang":"eng"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","citation":{"apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:66\">https://doi.org/10.15479/AT:ISTA:66</a>","mla":"von Wangenheim, Daniel, et al. <i>Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:66\">10.15479/AT:ISTA:66</a>.","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:66\">10.15479/AT:ISTA:66</a>","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017).","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. 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Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:04Z","citation":{"mla":"Hahn, David. <i>Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:73\">10.15479/AT:ISTA:73</a>.","apa":"Hahn, D. (2017). Source codes: Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:73\">https://doi.org/10.15479/AT:ISTA:73</a>","chicago":"Hahn, David. “Source Codes: Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:73\">https://doi.org/10.15479/AT:ISTA:73</a>.","ama":"Hahn D. Source codes: Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:73\">10.15479/AT:ISTA:73</a>","short":"D. Hahn, (2017).","ieee":"D. Hahn, “Source codes: Brittle fracture simulation with boundary elements for computer graphics.” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Source codes: Brittle fracture simulation with boundary elements for computer graphics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:73\">10.15479/AT:ISTA:73</a>."},"year":"2017","department":[{"_id":"ChWo"}],"article_processing_charge":"No","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source codes: Brittle fracture simulation with boundary elements for computer graphics","author":[{"last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Hahn, David"}],"file":[{"file_name":"IST-2017-73-v1+1_FractureRB_v1.1_2017_07_20_final_public.zip","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:02:57Z","file_size":199353471,"creator":"system","file_id":"5615","content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"2323a755842a3399cbc47d76545fc9a0"}],"keyword":["Boundary elements","brittle fracture","computer graphics","fracture simulation"],"date_updated":"2024-02-21T13:48:02Z","publisher":"Institute of Science and Technology Austria","datarep_id":"73","date_published":"2017-08-16T00:00:00Z","month":"08","has_accepted_license":"1"},{"publist_id":"7254","department":[{"_id":"SaSi"}],"article_processing_charge":"No","pubrep_id":"920","language":[{"iso":"eng"}],"publisher":"Association for Research in Vision and Ophthalmology","has_accepted_license":"1","author":[{"full_name":"Nickells, Robert","last_name":"Nickells","first_name":"Robert"},{"full_name":"Schmitt, Heather","first_name":"Heather","last_name":"Schmitt"},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"first_name":"Cassandra","last_name":"Schlamp","full_name":"Schlamp, Cassandra"}],"title":"AAV2 mediated transduction of the mouse retina after optic nerve injury","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T10:17:53Z","file_name":"IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf","checksum":"d7a7b6f1fa9211a04e5e65634a0265d9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5311","file_size":2955559,"creator":"system"}],"publication_status":"published","abstract":[{"text":"PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:47:04Z","publication_identifier":{"issn":["01460404"]},"citation":{"mla":"Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” <i>Investigative Ophthalmology and Visual Science</i>, vol. 58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104, doi:<a href=\"https://doi.org/10.1167/iovs.17-22634\">10.1167/iovs.17-22634</a>.","apa":"Nickells, R., Schmitt, H., Maes, M. E., &#38; Schlamp, C. (2017). AAV2 mediated transduction of the mouse retina after optic nerve injury. <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology. <a href=\"https://doi.org/10.1167/iovs.17-22634\">https://doi.org/10.1167/iovs.17-22634</a>","chicago":"Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology, 2017. <a href=\"https://doi.org/10.1167/iovs.17-22634\">https://doi.org/10.1167/iovs.17-22634</a>.","ama":"Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the mouse retina after optic nerve injury. <i>Investigative Ophthalmology and Visual Science</i>. 2017;58(14):6091-6104. doi:<a href=\"https://doi.org/10.1167/iovs.17-22634\">10.1167/iovs.17-22634</a>","short":"R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology and Visual Science 58 (2017) 6091–6104.","ieee":"R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction of the mouse retina after optic nerve injury,” <i>Investigative Ophthalmology and Visual Science</i>, vol. 58, no. 14. Association for Research in Vision and Ophthalmology, pp. 6091–6104, 2017.","ista":"Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 58(14), 6091–6104."},"quality_controlled":"1","_id":"557","page":"6091 - 6104","year":"2017","date_published":"2017-12-14T00:00:00Z","month":"12","intvolume":"        58","oa":1,"issue":"14","date_updated":"2023-10-10T14:06:18Z","publication":"Investigative Ophthalmology and Visual Science","doi":"10.1167/iovs.17-22634","oa_version":"Published Version","volume":58,"status":"public","day":"14","ddc":["576"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2018-12-11T11:47:10Z"},{"year":"2017","article_processing_charge":"No","department":[{"_id":"Bio"}],"keyword":["Cell migration","tracking","forward migration index","FMI"],"date_updated":"2024-02-21T13:47:14Z","author":[{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Forward migration indexes","file":[{"date_created":"2018-12-12T13:02:29Z","date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2017-75-v1+1_FMI.m","checksum":"cb7a2fa622460eca6231d659ce590e32","access_level":"open_access","relation":"main_file","file_size":799,"creator":"system","content_type":"application/octet-stream","file_id":"5596"}],"datarep_id":"75","date_published":"2017-10-04T00:00:00Z","has_accepted_license":"1","month":"10","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","doi":"10.15479/AT:ISTA:75","_id":"5570","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2018-12-12T12:31:35Z","ddc":["570"],"status":"public","day":"04","citation":{"apa":"Hauschild, R. (2017). Forward migration indexes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:75\">https://doi.org/10.15479/AT:ISTA:75</a>","mla":"Hauschild, Robert. <i>Forward Migration Indexes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:75\">10.15479/AT:ISTA:75</a>.","ieee":"R. Hauschild, “Forward migration indexes.” Institute of Science and Technology Austria, 2017.","ista":"Hauschild R. 2017. Forward migration indexes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:75\">10.15479/AT:ISTA:75</a>.","short":"R. Hauschild, (2017).","ama":"Hauschild R. Forward migration indexes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:75\">10.15479/AT:ISTA:75</a>","chicago":"Hauschild, Robert. “Forward Migration Indexes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:75\">https://doi.org/10.15479/AT:ISTA:75</a>."},"abstract":[{"text":"Matlab script to calculate the forward migration indexes (<d_y>/<L>) from TrackMate spot-statistics files.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:04Z","type":"research_data"},{"date_published":"2017-11-06T00:00:00Z","datarep_id":"78","has_accepted_license":"1","month":"11","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:48:16Z","title":"Data for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"file":[{"creator":"system","file_size":143697895,"content_type":"application/zip","file_id":"5618","checksum":"4520eb2b8379417ee916995719158f16","relation":"main_file","access_level":"open_access","file_name":"IST-2017-78-v1+1_Data.zip","date_created":"2018-12-12T13:03:00Z","date_updated":"2020-07-14T12:47:04Z"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"year":"2017","citation":{"mla":"Vicoso, Beatriz. <i>Data for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>.","apa":"Vicoso, B. (2017). Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>","chicago":"Vicoso, Beatriz. “Data for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:78\">https://doi.org/10.15479/AT:ISTA:78</a>.","ama":"Vicoso B. Data for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:78\">10.15479/AT:ISTA:78</a>","short":"B. Vicoso, (2017).","ista":"Vicoso B. 2017. 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Vicoso, “Data for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017."},"abstract":[{"text":"This folder contains all the data used in each of the main figures of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. \r\n","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:04Z","type":"research_data","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"5571","date_created":"2018-12-12T12:31:36Z","ddc":["576"],"status":"public","day":"06","doi":"10.15479/AT:ISTA:78","contributor":[{"contributor_type":"contact_person","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"related_material":{"record":[{"id":"542","status":"public","relation":"research_paper"}]},"oa_version":"Submitted Version"},{"date_updated":"2024-02-21T13:48:28Z","author":[{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"title":"Code for \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\"","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/zip","file_id":"5643","file_size":49823,"creator":"system","relation":"main_file","access_level":"open_access","checksum":"3e70a7bcd6ff0c38b79e4c8a7d137034","file_name":"IST-2017-79-v1+1_Code.zip","date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:05:15Z"}],"date_published":"2017-11-06T00:00:00Z","datarep_id":"79","has_accepted_license":"1","month":"11","publisher":"Institute of Science and Technology Austria","year":"2017","article_processing_charge":"No","department":[{"_id":"BeVi"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["576"],"_id":"5572","date_created":"2018-12-12T12:31:36Z","status":"public","day":"06","citation":{"mla":"Vicoso, Beatriz. <i>Code for “The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","apa":"Vicoso, B. (2017). Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>","chicago":"Vicoso, Beatriz. “Code for ‘The Genomic Characterization of the t-Haplotype, a Mouse Meiotic Driver, Highlights Its Complex History and Specialized Biology.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">https://doi.org/10.15479/AT:ISTA:79 </a>.","ieee":"B. Vicoso, “Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.’” Institute of Science and Technology Austria, 2017.","short":"B. Vicoso, (2017).","ista":"Vicoso B. 2017. Code for ‘The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>.","ama":"Vicoso B. Code for “The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:79 \">10.15479/AT:ISTA:79 </a>"},"abstract":[{"text":"Code described in the Supplementary Methods of \"The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology\" (Kelemen, R., Vicoso, B.)","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:05Z","type":"research_data","related_material":{"record":[{"id":"542","relation":"research_paper","status":"public"}]},"oa_version":"Submitted Version","doi":"10.15479/AT:ISTA:79 "},{"publication_identifier":{"issn":["1744-9561"]},"citation":{"apa":"Futo, M., Sell, M., Kutzer, M., &#38; Kurtz, J. (2017). Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>","mla":"Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>, vol. 13, no. 12, 0632, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>.","ieee":"M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming in the red flour beetle Tribolium castaneum,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","ista":"Futo M, Sell M, Kutzer M, Kurtz J. 2017. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 13(12), 0632.","short":"M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).","ama":"Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>","chicago":"Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>."},"type":"journal_article","abstract":[{"lang":"eng","text":"Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains."}],"scopus_import":"1","_id":"558","quality_controlled":"1","publication_status":"published","publisher":"The Royal Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"last_name":"Sell","first_name":"Marie","full_name":"Sell, Marie"},{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","first_name":"Megan","orcid":"0000-0002-8696-6978","last_name":"Kutzer","full_name":"Kutzer, Megan"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"title":"Specificity of oral immune priming in the red flour beetle Tribolium castaneum","article_processing_charge":"No","department":[{"_id":"SyCr"}],"publist_id":"7255","language":[{"iso":"eng"}],"article_type":"original","pmid":1,"volume":13,"date_created":"2018-12-11T11:47:10Z","status":"public","day":"01","doi":"10.1098/rsbl.2017.0632","publication":"Biology Letters","oa_version":"None","month":"12","intvolume":"        13","date_published":"2017-12-01T00:00:00Z","article_number":"0632","date_updated":"2023-10-18T06:42:25Z","issue":"12","external_id":{"pmid":["29237813"]},"year":"2017"},{"page":"357 - 379","conference":{"name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security","end_date":"2017-12-07","start_date":"2017-12-03","location":"Hong Kong, China"},"year":"2017","alternative_title":["LNCS"],"date_published":"2017-11-18T00:00:00Z","intvolume":"     10625","month":"11","date_updated":"2023-09-07T12:30:22Z","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2017/893.pdf","open_access":"1"}],"doi":"10.1007/978-3-319-70697-9_13","related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Submitted Version","volume":10625,"date_created":"2018-12-11T11:47:10Z","day":"18","status":"public","publist_id":"7257","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"publisher":"Springer","title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","author":[{"full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah"},{"last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"full_name":"Cohen, Bram","first_name":"Bram","last_name":"Cohen"},{"last_name":"Khilko","first_name":"Danylo","full_name":"Khilko, Danylo"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"isbn":["978-331970696-2"]},"citation":{"mla":"Abusalah, Hamza M., et al. <i>Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space</i>. Vol. 10625, Springer, 2017, pp. 357–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">10.1007/978-3-319-70697-9_13</a>.","apa":"Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., &#38; Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">https://doi.org/10.1007/978-3-319-70697-9_13</a>","chicago":"Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">https://doi.org/10.1007/978-3-319-70697-9_13</a>.","ama":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:<a href=\"https://doi.org/10.1007/978-3-319-70697-9_13\">10.1007/978-3-319-70697-9_13</a>","short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","ista":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.","ieee":"H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379."},"abstract":[{"text":"Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).","lang":"eng"}],"scopus_import":1,"type":"conference","_id":"559","quality_controlled":"1"},{"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.03229"}],"doi":"10.1098/rspa.2017.0104","ec_funded":1,"oa_version":"Submitted Version","volume":473,"date_created":"2018-12-11T11:47:11Z","day":"01","status":"public","year":"2017","date_published":"2017-11-01T00:00:00Z","intvolume":"       473","month":"11","article_number":"0104","date_updated":"2021-01-12T08:03:04Z","oa":1,"issue":"2207","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"publication_status":"published","citation":{"apa":"Gerencser, M., Jentzen, A., &#38; Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2017;473(2207). doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207. Royal Society of London, 2017.","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>."},"publication_identifier":{"issn":["13645021"]},"scopus_import":1,"abstract":[{"lang":"eng","text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions."}],"type":"journal_article","_id":"560","quality_controlled":"1","publist_id":"7256","department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"publisher":"Royal Society of London","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"first_name":"Arnulf","last_name":"Jentzen","full_name":"Jentzen, Arnulf"},{"full_name":"Salimova, Diyora","last_name":"Salimova","first_name":"Diyora"}],"title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions"},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"publist_id":"7253","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"}],"title":"Effects of mutations in phage restriction sites during escape from restriction–modification","publisher":"The Royal Society","publication_status":"published","project":[{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011"},{"grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"561","abstract":[{"text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.","lang":"eng"}],"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":["1744-9561"]},"citation":{"apa":"Pleska, M., &#38; Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>.","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0646\">10.1098/rsbl.2017.0646</a>","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0646\">https://doi.org/10.1098/rsbl.2017.0646</a>."},"year":"2017","external_id":{"pmid":["29237814"]},"oa":1,"issue":"12","date_updated":"2023-09-07T11:59:32Z","article_number":"20170646","acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","date_published":"2017-12-01T00:00:00Z","intvolume":"        13","month":"12","oa_version":"Published Version","related_material":{"record":[{"id":"9847","status":"public","relation":"research_data"},{"id":"202","relation":"dissertation_contains","status":"public"}]},"publication":"Biology Letters","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"doi":"10.1098/rsbl.2017.0646","status":"public","day":"01","date_created":"2018-12-11T11:47:11Z","volume":13,"pmid":1},{"series_title":"Courant Lecture Notes","page":"226","year":"2017","month":"01","intvolume":"        28","date_published":"2017-01-01T00:00:00Z","alternative_title":["Courant Lecture Notes"],"date_updated":"2022-05-24T06:57:28Z","doi":"10.1090/cln/028","ec_funded":1,"oa_version":"None","volume":28,"date_created":"2018-12-11T11:47:13Z","status":"public","day":"01","article_processing_charge":"No","publist_id":"7247","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"publisher":"American Mathematical Society","title":"A Dynamical Approach to Random Matrix Theory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng"}],"project":[{"call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"eisbn":["978-1-4704-4194-4"],"isbn":["9-781-4704-3648-3"]},"citation":{"apa":"Erdös, L., &#38; Yau, H. (2017). <i>A Dynamical Approach to Random Matrix Theory</i> (Vol. 28). American Mathematical Society. <a href=\"https://doi.org/10.1090/cln/028\">https://doi.org/10.1090/cln/028</a>","mla":"Erdös, László, and Horng Yau. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol. 28, American Mathematical Society, 2017, doi:<a href=\"https://doi.org/10.1090/cln/028\">10.1090/cln/028</a>.","ama":"Erdös L, Yau H. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol 28. American Mathematical Society; 2017. doi:<a href=\"https://doi.org/10.1090/cln/028\">10.1090/cln/028</a>","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017.","ieee":"L. Erdös and H. Yau, <i>A Dynamical Approach to Random Matrix Theory</i>, vol. 28. American Mathematical Society, 2017.","ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","chicago":"Erdös, László, and Horng Yau. <i>A Dynamical Approach to Random Matrix Theory</i>. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/cln/028\">https://doi.org/10.1090/cln/028</a>."},"type":"book","abstract":[{"lang":"eng","text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n"}],"_id":"567","quality_controlled":"1"}]