[{"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"first_name":"Kristin","last_name":"Hagel","full_name":"Hagel, Kristin"},{"last_name":"Milinski","first_name":"Manfred","full_name":"Milinski, Manfred"}],"citation":{"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>","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>.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","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>","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","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>."},"year":"2016","day":"04","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-21T16:59:01Z","_id":"9868","department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1322"}]},"doi":"10.1371/journal.pone.0163867.s009","title":"Experimental data","abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"date_published":"2016-10-04T00:00:00Z","publisher":"Public Library of Science","status":"public","month":"10","date_created":"2021-08-10T08:45:00Z"},{"title":"Error bound on an estimator of position","department":[{"_id":"GaTk"}],"_id":"9869","related_material":{"record":[{"id":"1270","relation":"used_in_publication","status":"public"}]},"doi":"10.1371/journal.pone.0163628.s001","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"citation":{"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>","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>.","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>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","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>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","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>"},"article_processing_charge":"No","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-21T16:56:40Z","year":"2016","day":"27","month":"09","date_created":"2021-08-10T08:53:48Z","status":"public","date_published":"2016-09-27T00:00:00Z","publisher":"Public Library of Science"},{"year":"2016","day":"27","oa_version":"Published Version","date_updated":"2023-02-21T16:56:40Z","type":"research_data_reference","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","citation":{"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>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","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>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","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>","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>.","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>"},"abstract":[{"lang":"eng","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."}],"department":[{"_id":"GaTk"}],"_id":"9870","doi":"10.1371/journal.pone.0163628.s002","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"title":"Computation of positional information in an Ising model","publisher":"Public Library of Science","date_published":"2016-09-27T00:00:00Z","status":"public","month":"09","date_created":"2021-08-10T09:23:45Z"},{"article_processing_charge":"No","author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in a Discrete Morphogen Field</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","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>","ista":"Hillenbrand P, Gerland U, 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\">10.1371/journal.pone.0163628.s003</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>"},"year":"2016","day":"27","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-21T16:56:40Z","_id":"9871","department":[{"_id":"GaTk"}],"doi":"10.1371/journal.pone.0163628.s003","related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"title":"Computation of positional information in a discrete morphogen field","abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"publisher":"Public Library of Science","status":"public","month":"09","date_created":"2021-08-10T09:27:35Z"},{"related_material":{"record":[{"id":"1250","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pgen.1005974.s015","department":[{"_id":"CaGu"}],"_id":"9873","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","day":"19","year":"2016","type":"research_data_reference","date_updated":"2023-02-21T16:50:13Z","oa_version":"Published Version","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Boehm, Alex","last_name":"Boehm","first_name":"Alex"},{"last_name":"Arnoldini","first_name":"Markus","full_name":"Arnoldini, Markus"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"full_name":"Röösli, Thomas","last_name":"Röösli","first_name":"Thomas"},{"full_name":"Bigosch, Colette","last_name":"Bigosch","first_name":"Colette"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"citation":{"ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, 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\">10.1371/journal.pgen.1005974.s015</a>.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","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>.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","mla":"Boehm, Alex, et al. <i>Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">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>"},"status":"public","date_created":"2021-08-10T09:42:34Z","month":"04","publisher":"Public Library of Science"},{"scopus_import":1,"publist_id":"6298","alternative_title":["Advances in Neural Information Processing Systems"],"intvolume":"        29","status":"public","conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","start_date":"2016-12-05","location":"Barcelona, Spain"},"month":"12","date_created":"2018-12-11T11:50:03Z","volume":29,"page":"1965-1973","date_published":"2016-12-01T00:00:00Z","publisher":"Neural Information Processing Systems","department":[{"_id":"GaTk"}],"_id":"1082","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck","relation":"other"}]},"oa":1,"title":"Relevant sparse codes with variational information bottleneck","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"publication_status":"published","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07332"}],"citation":{"ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","mla":"Chalk, Matthew J., et al. <i>Relevant Sparse Codes with Variational Information Bottleneck</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems."},"year":"2016","day":"01","oa_version":"Preprint","date_updated":"2021-01-12T06:48:09Z","type":"conference"},{"intvolume":"        27","publist_id":"6297","month":"04","date_created":"2018-12-11T11:50:03Z","status":"public","date_published":"2016-04-12T00:00:00Z","volume":27,"page":"2318 - 2334","issue":"3","publisher":"Oxford University Press","publication":"Cerebral Cortex","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","_id":"1083","department":[{"_id":"RySh"}],"doi":"10.1093/cercor/bhw090","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"publication_status":"published","citation":{"apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>","mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>.","ieee":"S. Booker <i>et al.</i>, “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” <i>Cerebral Cortex</i>, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. 2016;27(3):2318-2334. doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334."},"quality_controlled":"1","author":[{"full_name":"Booker, Sam","first_name":"Sam","last_name":"Booker"},{"last_name":"Althof","first_name":"Daniel","full_name":"Althof, Daniel"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"last_name":"Loreth","first_name":"Desiree","full_name":"Loreth, Desiree"},{"last_name":"Müller","first_name":"Johanna","full_name":"Müller, Johanna"},{"full_name":"Unger, Andreas","last_name":"Unger","first_name":"Andreas"},{"full_name":"Fakler, Bernd","first_name":"Bernd","last_name":"Fakler"},{"full_name":"Varro, Andrea","last_name":"Varro","first_name":"Andrea"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vida, Imre","last_name":"Vida","first_name":"Imre"},{"first_name":"Ákos","last_name":"Kulik","full_name":"Kulik, Ákos"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2021-01-12T06:48:09Z","type":"journal_article","year":"2016","day":"12"},{"publist_id":"6286","intvolume":"        58","article_number":"24","status":"public","month":"08","conference":{"start_date":"2016-08-22","location":"Krakow; Poland","end_date":"2016-08-26","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"date_created":"2018-12-11T11:50:05Z","pubrep_id":"795","volume":58,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:17:31Z","_id":"1090","oa":1,"ddc":["004"],"title":"Nested weighted limit-average automata of bounded width","abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"publication_status":"published","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Nested Weighted Limit-Average Automata of Bounded Width</i>. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland, 2016, vol. 58.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 24.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>."},"year":"2016","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"},"scopus_import":1,"alternative_title":["LIPIcs"],"file":[{"file_id":"5286","date_updated":"2018-12-12T10:17:31Z","access_level":"open_access","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","date_created":"2018-12-12T10:17:31Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":564560}],"date_published":"2016-08-01T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2016.24","ec_funded":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","date_updated":"2021-01-12T06:48:12Z","type":"conference"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","type":"conference","date_updated":"2023-09-07T11:58:33Z","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2016.20","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"has_accepted_license":"1","ec_funded":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","date_published":"2016-08-01T00:00:00Z","file":[{"file_id":"4895","date_updated":"2018-12-12T10:11:39Z","access_level":"open_access","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","date_created":"2018-12-12T10:11:39Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":501827}],"scopus_import":1,"alternative_title":["LIPIcs"],"author":[{"last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"},{"first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"quality_controlled":"1","citation":{"mla":"Daca, Przemyslaw, et al. <i>Linear Distances between Markov Chains</i>. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>"},"year":"2016","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"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"oa":1,"ddc":["004"],"_id":"1093","title":"Linear distances between Markov chains","publication_status":"published","abstract":[{"text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. ","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"volume":59,"pubrep_id":"794","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:11:39Z","publist_id":"6283","intvolume":"        59","status":"public","article_number":"20","date_created":"2018-12-11T11:50:06Z","conference":{"location":"Quebec City; Canada","start_date":"2016-08-23","name":"CONCUR: Concurrency Theory","end_date":"2016-08-26"},"month":"08"},{"page":"203 - 216","date_published":"2016-08-12T00:00:00Z","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"alternative_title":["Methods in Molecular Biology"],"day":"12","type":"book_chapter","date_updated":"2023-09-05T14:09:01Z","oa_version":"None","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6352-2_12","department":[{"_id":"RySh"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"publisher":"Springer","volume":1474,"status":"public","date_created":"2018-12-11T11:50:06Z","month":"08","publist_id":"6281","intvolume":"      1474","year":"2016","quality_controlled":"1","author":[{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"citation":{"apa":"Harada, H., &#38; Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In <i>High-Resolution Imaging of Cellular Proteins</i> (Vol. 1474, pp. 203–216). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–16, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>.","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In <i>High-Resolution Imaging of Cellular Proteins</i>, 1474:203–16. Springer, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>.","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: <i>High-Resolution Imaging of Cellular Proteins</i>. Vol 1474. Springer; 2016:203-216. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–216."},"publication_status":"published","abstract":[{"lang":"eng","text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face."}],"project":[{"call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches"}],"_id":"1094","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","publication":"High-Resolution Imaging of Cellular Proteins"},{"abstract":[{"lang":"eng","text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. "}],"publication_status":"published","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"1095","ddc":["004"],"oa":1,"title":"Local linearizability for concurrent container-type data structures","publication":"Leibniz International Proceedings in Informatics","year":"2016","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"},"author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Holzer, Andreas","last_name":"Holzer","first_name":"Andreas"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"first_name":"Michael","last_name":"Lippautz","full_name":"Lippautz, Michael"},{"last_name":"Payer","first_name":"Hannes","full_name":"Payer, Hannes"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"},{"full_name":"Veith, Helmut","first_name":"Helmut","last_name":"Veith"}],"quality_controlled":"1","citation":{"ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>","ieee":"A. Haas <i>et al.</i>, “Local linearizability for concurrent container-type data structures,” in <i>Leibniz International Proceedings in Informatics</i>, Quebec City; Canada, 2016, vol. 59.","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” <i>Leibniz International Proceedings in Informatics</i>, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>."},"article_number":"6","status":"public","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2016-08-26","location":"Quebec City; Canada","start_date":"2016-08-23"},"month":"08","date_created":"2018-12-11T11:50:07Z","publist_id":"6280","intvolume":"        59","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:10:10Z","pubrep_id":"793","volume":59,"acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","has_accepted_license":"1","department":[{"_id":"ToHe"}],"doi":"10.4230/LIPIcs.CONCUR.2016.6","language":[{"iso":"eng"}],"ec_funded":1,"day":"01","oa_version":"Published Version","type":"conference","date_updated":"2021-01-12T06:48:14Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LIPIcs"],"file":[{"content_type":"application/pdf","creator":"system","file_size":589747,"relation":"main_file","date_created":"2018-12-12T10:10:10Z","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","access_level":"open_access","date_updated":"2018-12-12T10:10:10Z","file_id":"4795"}],"date_published":"2016-08-01T00:00:00Z"},{"scopus_import":1,"publist_id":"6279","intvolume":"        37","status":"public","month":"06","date_created":"2018-12-11T11:50:07Z","page":"493 - 506","volume":37,"issue":"6","date_published":"2016-06-20T00:00:00Z","publisher":"Cell Press","department":[{"_id":"CaHe"}],"_id":"1096","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7186"}]},"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2016.05.024","title":"Actin rings of power","publication":"Developmental Cell","publication_status":"published","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","first_name":"Cornelia","last_name":"Schwayer"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora"},{"id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","first_name":"Jana","last_name":"Slovakova"},{"first_name":"Roland","last_name":"Kardos","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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>","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 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>.","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","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.","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>"},"year":"2016","day":"20","oa_version":"None","date_updated":"2023-09-07T12:56:41Z","type":"journal_article"},{"department":[{"_id":"BeBi"}],"has_accepted_license":"1","doi":"10.1145/2980179.2982427","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","date_updated":"2021-01-12T06:48:15Z","type":"conference","scopus_import":1,"alternative_title":["ACM Transactions on Graphics"],"file":[{"file_name":"IST-2017-759-v1+1_copter.pdf","access_level":"open_access","file_id":"5298","date_updated":"2018-12-12T10:17:42Z","content_type":"application/pdf","creator":"system","file_size":33114420,"relation":"main_file","date_created":"2018-12-12T10:17:42Z"}],"date_published":"2016-11-01T00:00:00Z","_id":"1097","oa":1,"ddc":["006"],"title":"Computational multicopter design","abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"publication_status":"published","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation"}],"quality_controlled":"1","author":[{"full_name":"Du, Tao","last_name":"Du","first_name":"Tao"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"},{"last_name":"Zhu","first_name":"Bo","full_name":"Zhu, Bo"},{"last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"citation":{"ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., &#38; Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>","mla":"Du, Tao, et al. <i>Computational Multicopter Design</i>. Vol. 35, no. 6, 227, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>."},"year":"2016","publist_id":"6278","intvolume":"        35","status":"public","article_number":"227","month":"11","conference":{"start_date":"2016-12-05","location":"Macao, China","end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"date_created":"2018-12-11T11:50:07Z","pubrep_id":"759","issue":"6","volume":35,"publisher":"ACM","file_date_updated":"2018-12-12T10:17:42Z"},{"citation":{"short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems; 2016:3619-3627.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","apa":"Pentina, A., &#38; Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems."},"author":[{"last_name":"Pentina","first_name":"Anastasia","full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Urner, Ruth","first_name":"Ruth","last_name":"Urner"}],"quality_controlled":"1","year":"2016","title":"Lifelong learning with weighted majority votes","_id":"1098","oa":1,"ddc":["006"],"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"publication_status":"published","pubrep_id":"775","volume":29,"file_date_updated":"2018-12-12T10:12:43Z","publisher":"Neural Information Processing Systems","intvolume":"        29","publist_id":"6277","conference":{"location":"Barcelona, Spain","start_date":"2016-12-05","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"month":"12","date_created":"2018-12-11T11:50:08Z","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"conference","date_updated":"2021-01-12T06:48:15Z","day":"01","ec_funded":1,"has_accepted_license":"1","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","file":[{"access_level":"open_access","file_name":"IST-2017-775-v1+1_main.pdf","date_updated":"2018-12-12T10:12:42Z","file_id":"4961","creator":"system","content_type":"application/pdf","file_size":237111,"date_created":"2018-12-12T10:12:42Z","relation":"main_file"},{"access_level":"open_access","file_name":"IST-2017-775-v1+2_supplementary.pdf","file_id":"4962","date_updated":"2018-12-12T10:12:43Z","creator":"system","content_type":"application/pdf","file_size":185818,"date_created":"2018-12-12T10:12:43Z","relation":"main_file"}],"date_published":"2016-12-01T00:00:00Z","page":"3619-3627","alternative_title":["Advances in Neural Information Processing Systems"],"scopus_import":1},{"date_published":"2016-11-01T00:00:00Z","file":[{"date_updated":"2018-12-12T10:12:01Z","file_id":"4918","file_name":"IST-2017-760-v1+1_flexmolds.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:01Z","content_type":"application/pdf","creator":"system","file_size":11122029}],"scopus_import":1,"alternative_title":["ACM Transactions on Graphics"],"day":"01","type":"conference","date_updated":"2021-01-12T06:48:16Z","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford  3D  Scanning  Repository.   The  bimba,  fertility  and  elephant models are courtesy of the AIM@SHAPE Shape Repository.  \r\nThis project has received funding from the European Union’s Horizon 2020  research  and  innovation  programme  under  grant  agreement\r\nNo. 645599.","language":[{"iso":"eng"}],"doi":"10.1145/2980179.2982397","has_accepted_license":"1","department":[{"_id":"BeBi"}],"ec_funded":1,"publisher":"ACM","file_date_updated":"2018-12-12T10:12:01Z","volume":35,"issue":"6","pubrep_id":"760","status":"public","article_number":"223","date_created":"2018-12-11T11:50:08Z","conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","end_date":"2016-12-08","location":"Macao, China","start_date":"2016-12-05"},"month":"11","publist_id":"6276","intvolume":"        35","year":"2016","author":[{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"}],"quality_controlled":"1","citation":{"mla":"Malomo, Luigi, et al. <i>FlexMolds: Automatic Design of Flexible Shells for Molding</i>. Vol. 35, no. 6, 223, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>.","apa":"Malomo, L., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6."},"publication_status":"published","abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation"}],"oa":1,"ddc":["000","005"],"_id":"1099","title":"FlexMolds: Automatic design of flexible shells for molding"},{"day":"19","date_updated":"2024-03-25T23:30:13Z","type":"journal_article","oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","doi":"10.1016/j.celrep.2016.06.036","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"SSU"}],"ec_funded":1,"page":"866 - 877","date_published":"2016-07-19T00:00:00Z","file":[{"access_level":"open_access","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","date_updated":"2018-12-12T10:11:04Z","file_id":"4857","file_size":3921947,"content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:11:04Z","relation":"main_file"}],"scopus_import":1,"year":"2016","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"},"quality_controlled":"1","author":[{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","first_name":"Keisuke","last_name":"Sako"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Barone"},{"last_name":"Inglés Prieto","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mueller","first_name":"Patrick","full_name":"Mueller, Patrick"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","first_name":"Daniel"},{"full_name":"Galande, Sanjeev","first_name":"Sanjeev","last_name":"Galande"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"citation":{"ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>."},"publication_status":"published","abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"}],"oa":1,"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"ddc":["570","576"],"_id":"1100","title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","publication":"Cell Reports","publisher":"Cell Press","file_date_updated":"2018-12-12T10:11:04Z","volume":16,"issue":"3","pubrep_id":"754","status":"public","date_created":"2018-12-11T11:50:08Z","month":"07","publist_id":"6275","intvolume":"        16"},{"publisher":"American Chemical Society","date_published":"2016-11-10T00:00:00Z","volume":1,"page":"1286 - 1290","issue":"11","month":"11","date_created":"2018-12-11T11:50:09Z","status":"public","intvolume":"         1","scopus_import":"1","publist_id":"6274","oa_version":"None","type":"journal_article","date_updated":"2023-03-30T11:32:33Z","year":"2016","day":"10","citation":{"apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>.","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. 2016;1(11):1286-1290. doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>","ieee":"J. Mitchell <i>et al.</i>, “Rangefinder: A semisynthetic FRET sensor design algorithm,” <i>ACS SENSORS</i>, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016."},"quality_controlled":"1","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","abstract":[{"lang":"eng","text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of &gt;300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest."}],"publication_status":"published","publication":"ACS SENSORS","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","department":[{"_id":"HaJa"}],"_id":"1101","doi":"10.1021/acssensors.6b00576","language":[{"iso":"eng"}]},{"publisher":"BMVA Press","volume":"2016-September","status":"public","date_created":"2018-12-11T11:50:09Z","conference":{"location":"York, United Kingdom","start_date":"2016-09-19","end_date":"2016-09-22","name":"BMVC: British Machine Vision Conference"},"month":"09","publist_id":"6273","year":"2016","author":[{"first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}],"citation":{"apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In <i>Proceedings of the British Machine Vision Conference 2016</i> (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” <i>Proceedings of the British Machine Vision Conference 2016</i>, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In <i>Proceedings of the British Machine Vision Conference 2016</i>, 2016–September:92.1-92.12. BMVA Press, 2016. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>.","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in <i>Proceedings of the British Machine Vision Conference 2016</i>, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: <i>Proceedings of the British Machine Vision Conference 2016</i>. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>"},"publication_status":"published","abstract":[{"text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation.","lang":"eng"}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"_id":"1102","title":"Improving weakly-supervised object localization by micro-annotation","publication":"Proceedings of the British Machine Vision Conference 2016","page":"92.1-92.12","date_published":"2016-09-01T00:00:00Z","scopus_import":1,"day":"01","type":"conference","date_updated":"2021-01-12T06:48:18Z","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","language":[{"iso":"eng"}],"doi":"10.5244/C.30.92","department":[{"_id":"ChLa"}],"ec_funded":1},{"publisher":"IEEE","date_published":"2016-12-27T00:00:00Z","date_created":"2018-12-11T11:50:09Z","conference":{"end_date":"2016-11-20","name":"MEMOCODE: International Conference on Formal Methods and Models for System Design","start_date":"2016-11-18","location":"Kanpur, India "},"month":"12","status":"public","article_number":"7797741","publist_id":"6272","scopus_import":1,"type":"conference","date_updated":"2021-01-12T06:48:18Z","oa_version":"Preprint","day":"27","year":"2016","main_file_link":[{"url":"https://arxiv.org/abs/1606.05473","open_access":"1"}],"citation":{"apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., &#38; Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>","mla":"Gurung, Amit, et al. <i>Parallel Reachability Analysis for Hybrid Systems</i>. 7797741, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>.","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: International Conference on Formal Methods and Models for System Design, 7797741."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Amit","last_name":"Gurung","full_name":"Gurung, Amit"},{"full_name":"Deka, Arup","last_name":"Deka","first_name":"Arup"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"first_name":"Rajarshi","last_name":"Ray","full_name":"Ray, Rajarshi"}],"quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","publication_status":"published","abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"title":"Parallel reachability analysis for hybrid systems","ec_funded":1,"doi":"10.1109/MEMCOD.2016.7797741","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"_id":"1103"},{"intvolume":"        29","publist_id":"6265","date_created":"2018-12-11T11:50:10Z","conference":{"start_date":"2016-12-05","location":"Barcelona; Spain","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"month":"12","status":"public","volume":29,"publisher":"Neural Information Processing Systems","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","_id":"1105","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"citation":{"ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18."},"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"quality_controlled":"1","author":[{"last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"year":"2016","alternative_title":["Advances in Neural Information Processing Systems"],"scopus_import":1,"date_published":"2016-12-01T00:00:00Z","page":"3610-3618","ec_funded":1,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","date_updated":"2021-01-12T06:48:19Z","oa_version":"None","day":"01"}]