[{"doi":"10.1371/journal.pone.0163867.s008","_id":"9867","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1322"}]},"date_created":"2021-08-10T08:42:00Z","title":"Experimental game instructions","citation":{"apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>."},"article_processing_charge":"No","year":"2016","date_updated":"2023-02-21T16:59:01Z","department":[{"_id":"KrCh"}],"type":"research_data_reference","status":"public","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"day":"04","oa_version":"Published Version","month":"10","author":[{"first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"first_name":"Kristin","full_name":"Hagel, Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}]},{"author":[{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian"},{"full_name":"Hagel, Kristin","first_name":"Kristin","last_name":"Hagel"},{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"}],"month":"10","day":"04","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The raw data file containing the experimental decisions of all our study subjects."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","type":"research_data_reference","status":"public","date_published":"2016-10-04T00:00:00Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-21T16:59:01Z","article_processing_charge":"No","year":"2016","date_created":"2021-08-10T08:45:00Z","title":"Experimental data","citation":{"chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","short":"C. Hilbe, K. Hagel, M. Milinski, (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>","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>"},"related_material":{"record":[{"status":"public","id":"1322","relation":"used_in_publication"}]},"_id":"9868","doi":"10.1371/journal.pone.0163867.s009"},{"author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"abstract":[{"text":"A lower bound on the error of a positional estimator with limited positional information is derived.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","oa_version":"Published Version","month":"09","department":[{"_id":"GaTk"}],"date_published":"2016-09-27T00:00:00Z","status":"public","type":"research_data_reference","publisher":"Public Library of Science","title":"Error bound on an estimator of position","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>","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>","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","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>.","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>."},"date_created":"2021-08-10T08:53:48Z","year":"2016","article_processing_charge":"No","date_updated":"2023-02-21T16:56:40Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1270"}]},"_id":"9869","doi":"10.1371/journal.pone.0163628.s001"},{"publisher":"American Physical Society","type":"journal_article","status":"public","date_published":"2016-10-17T00:00:00Z","extern":1,"quality_controlled":0,"volume":94,"month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1512.08523","open_access":"1"}],"day":"17","abstract":[{"lang":"eng","text":"In contrast to bulk FeSe, which exhibits nematic order and low temperature superconductivity, highly doped FeSe reverses the situation, having high temperature superconductivity appearing alongside a suppression of nematic order. To investigate this phenomenon, we study a minimal electronic model of FeSe, with interactions that enhance nematic fluctuations. This model is sign problem free, and is simulated using determinant quantum Monte Carlo (DQMC). We developed a DQMC algorithm with parallel tempering, which proves to be an efficient source of global updates and allows us to access the region of strong interactions. Over a wide range of intermediate couplings, we observe superconductivity with an extended s-wave order parameter, along with enhanced, but short-ranged, q=(0,0) ferro-orbital (nematic) order. These results are consistent with approximate weak-coupling treatments that predict that nematic fluctuations lead to superconducting pairing. Surprisingly, in the parameter range under study, we do not observe nematic long-range order. Instead, at stronger coupling an unusual insulating phase with q=(π,π) antiferro-orbital order appears, which is missed by weak-coupling approximations."}],"author":[{"last_name":"Dumitrescu","first_name":"Philipp","full_name":"Dumitrescu, Philipp T"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Maksym Serbyn"},{"last_name":"Scalettar","full_name":"Scalettar, Richard T","first_name":"Richard"},{"full_name":"Vishwanath, Ashvin K","first_name":"Ashvin","last_name":"Vishwanath"}],"publication_status":"published","publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.94.155127","_id":"987","intvolume":"        94","date_updated":"2021-01-12T08:22:27Z","acknowledgement":"We thank S. Gazit for numerous discussions. This research was supported by the Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M.S.), the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Grant No. DE-SC0014671 (R.T.S.), and a Simons Investigator grant (A.V.).","oa":1,"year":"2016","issue":"15","title":"Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study","publist_id":"6413","citation":{"mla":"Dumitrescu, Philipp, et al. “Superconductivity and Nematic Fluctuations in a Model of Doped FeSe Monolayers: Determinant Quantum Monte Carlo Study.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 15, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.155127\">10.1103/PhysRevB.94.155127</a>.","ista":"Dumitrescu P, Serbyn M, Scalettar R, Vishwanath A. 2016. Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study. Physical Review B - Condensed Matter and Materials Physics. 94(15).","chicago":"Dumitrescu, Philipp, Maksym Serbyn, Richard Scalettar, and Ashvin Vishwanath. “Superconductivity and Nematic Fluctuations in a Model of Doped FeSe Monolayers: Determinant Quantum Monte Carlo Study.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.155127\">https://doi.org/10.1103/PhysRevB.94.155127</a>.","ama":"Dumitrescu P, Serbyn M, Scalettar R, Vishwanath A. Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;94(15). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.155127\">10.1103/PhysRevB.94.155127</a>","ieee":"P. Dumitrescu, M. Serbyn, R. Scalettar, and A. Vishwanath, “Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 15. American Physical Society, 2016.","short":"P. Dumitrescu, M. Serbyn, R. Scalettar, A. Vishwanath, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","apa":"Dumitrescu, P., Serbyn, M., Scalettar, R., &#38; Vishwanath, A. (2016). Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.155127\">https://doi.org/10.1103/PhysRevB.94.155127</a>"},"date_created":"2018-12-11T11:49:33Z"},{"department":[{"_id":"GaTk"}],"date_published":"2016-09-27T00:00:00Z","status":"public","type":"research_data_reference","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","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."}],"oa_version":"Published Version","day":"27","month":"09","author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1371/journal.pone.0163628.s002","_id":"9870","related_material":{"record":[{"id":"1270","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-10T09:23:45Z","title":"Computation of positional information in an Ising model","citation":{"apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>","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>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","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>","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"year":"2016","article_processing_charge":"No","date_updated":"2023-02-21T16:56:40Z"},{"doi":"10.1371/journal.pone.0163628.s003","_id":"9871","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"date_updated":"2023-02-21T16:56:40Z","year":"2016","article_processing_charge":"No","title":"Computation of positional information in a discrete morphogen field","citation":{"apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. 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>","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","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>.","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>.","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>."},"date_created":"2021-08-10T09:27:35Z","publisher":"Public Library of Science","status":"public","type":"research_data_reference","department":[{"_id":"GaTk"}],"month":"09","oa_version":"Published Version","day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"The positional information in a discrete morphogen field with Gaussian noise is computed."}],"author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}]},{"author":[{"last_name":"Boehm","full_name":"Boehm, Alex","first_name":"Alex"},{"last_name":"Arnoldini","full_name":"Arnoldini, Markus","first_name":"Markus"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","orcid":"0000-0001-5396-4346"},{"full_name":"Röösli, Thomas","first_name":"Thomas","last_name":"Röösli"},{"last_name":"Bigosch","first_name":"Colette","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"month":"04","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"19","oa_version":"Published Version","type":"research_data_reference","status":"public","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"article_processing_charge":"No","year":"2016","date_updated":"2023-02-21T16:50:13Z","date_created":"2021-08-10T09:42:34Z","citation":{"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>","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>.","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>.","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>.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","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.","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>"},"title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","related_material":{"record":[{"id":"1250","relation":"used_in_publication","status":"public"}]},"_id":"9873","doi":"10.1371/journal.pgen.1005974.s015"},{"language":[{"iso":"eng"}],"_id":"1082","year":"2016","oa":1,"date_updated":"2021-01-12T06:48:09Z","title":"Relevant sparse codes with variational information bottleneck","date_created":"2018-12-11T11:50:03Z","citation":{"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.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, 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.","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.","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."},"publist_id":"6298","scopus_import":1,"related_material":{"link":[{"url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck","relation":"other"}]},"intvolume":"        29","type":"conference","status":"public","date_published":"2016-12-01T00:00:00Z","alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems","quality_controlled":"1","volume":29,"department":[{"_id":"GaTk"}],"page":"1965-1973","publication_status":"published","author":[{"full_name":"Chalk, Matthew J","first_name":"Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"month":"12","conference":{"location":"Barcelona, Spain","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"oa_version":"Preprint","day":"01"},{"publisher":"Oxford University Press","status":"public","date_published":"2016-04-12T00:00:00Z","type":"journal_article","page":"2318 - 2334","department":[{"_id":"RySh"}],"volume":27,"quality_controlled":"1","publication_status":"published","author":[{"first_name":"Sam","full_name":"Booker, Sam","last_name":"Booker"},{"last_name":"Althof","full_name":"Althof, Daniel","first_name":"Daniel"},{"last_name":"Gross","full_name":"Gross, Anna","first_name":"Anna"},{"last_name":"Loreth","first_name":"Desiree","full_name":"Loreth, Desiree"},{"last_name":"Müller","full_name":"Müller, Johanna","first_name":"Johanna"},{"last_name":"Unger","full_name":"Unger, Andreas","first_name":"Andreas"},{"full_name":"Fakler, Bernd","first_name":"Bernd","last_name":"Fakler"},{"first_name":"Andrea","full_name":"Varro, Andrea","last_name":"Varro"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"first_name":"Martin","full_name":"Gassmann, Martin","last_name":"Gassmann"},{"last_name":"Bettler","full_name":"Bettler, Bernhard","first_name":"Bernhard"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Imre","full_name":"Vida, Imre","last_name":"Vida"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"}],"month":"04","oa_version":"None","day":"12","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"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1083","language":[{"iso":"eng"}],"publication":"Cerebral Cortex","doi":"10.1093/cercor/bhw090","date_updated":"2021-01-12T06:48:09Z","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. ","issue":"3","year":"2016","citation":{"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>","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.","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.","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>.","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>.","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>"},"date_created":"2018-12-11T11:50:03Z","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","publist_id":"6297","intvolume":"        27"},{"doi":"10.1080/19490992.2016.1201620","publication":"BioArchitecture","_id":"1088","language":[{"iso":"eng"}],"intvolume":"         6","citation":{"apa":"Uhler, C., &#38; Shivashankar, G. V. (2016). Geometric control and modeling of genome reprogramming. <i>BioArchitecture</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19490992.2016.1201620\">https://doi.org/10.1080/19490992.2016.1201620</a>","mla":"Uhler, Caroline, and G. V. Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” <i>BioArchitecture</i>, vol. 6, no. 4, Taylor &#38; Francis, 2016, pp. 76–84, doi:<a href=\"https://doi.org/10.1080/19490992.2016.1201620\">10.1080/19490992.2016.1201620</a>.","chicago":"Uhler, Caroline, and G V Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” <i>BioArchitecture</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/19490992.2016.1201620\">https://doi.org/10.1080/19490992.2016.1201620</a>.","ista":"Uhler C, Shivashankar GV. 2016. Geometric control and modeling of genome reprogramming. BioArchitecture. 6(4), 76–84.","short":"C. Uhler, G.V. Shivashankar, BioArchitecture 6 (2016) 76–84.","ama":"Uhler C, Shivashankar GV. Geometric control and modeling of genome reprogramming. <i>BioArchitecture</i>. 2016;6(4):76-84. doi:<a href=\"https://doi.org/10.1080/19490992.2016.1201620\">10.1080/19490992.2016.1201620</a>","ieee":"C. Uhler and G. V. Shivashankar, “Geometric control and modeling of genome reprogramming,” <i>BioArchitecture</i>, vol. 6, no. 4. Taylor &#38; Francis, pp. 76–84, 2016."},"title":"Geometric control and modeling of genome reprogramming","publist_id":"6289","date_created":"2018-12-11T11:50:05Z","date_updated":"2021-01-12T06:48:11Z","issue":"4","year":"2016","page":"76 - 84","extern":"1","quality_controlled":"1","volume":6,"publisher":"Taylor & Francis","type":"journal_article","date_published":"2016-07-27T00:00:00Z","status":"public","oa_version":"None","day":"27","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.","lang":"eng"}],"month":"07","publication_status":"published","author":[{"first_name":"Caroline","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","orcid":"0000-0002-7008-0216"},{"last_name":"Shivashankar","first_name":"G V","full_name":"Shivashankar, G V"}]},{"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"volume":58,"quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_published":"2016-08-01T00:00:00Z","license":"https://creativecommons.org/licenses/by/4.0/","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["004"],"_id":"1090","file_date_updated":"2018-12-12T10:17:31Z","doi":"10.4230/LIPIcs.MFCS.2016.24","citation":{"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>.","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.","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>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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>","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>"},"publist_id":"6286","date_created":"2018-12-11T11:50:05Z","year":"2016","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.","article_number":"24","ec_funded":1,"type":"conference","status":"public","alternative_title":["LIPIcs"],"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","file_id":"5286","date_updated":"2018-12-12T10:17:31Z","date_created":"2018-12-12T10:17:31Z","creator":"system","content_type":"application/pdf","file_size":564560,"access_level":"open_access","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","month":"08","conference":{"start_date":"2016-08-22","name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2016-08-26","location":"Krakow; Poland"},"language":[{"iso":"eng"}],"title":"Nested weighted limit-average automata of bounded width","date_updated":"2021-01-12T06:48:12Z","pubrep_id":"795","oa":1,"intvolume":"        58","has_accepted_license":"1","scopus_import":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["004"],"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"}],"publication_status":"published","date_published":"2016-08-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","volume":59,"department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"article_number":"20","related_material":{"record":[{"id":"1155","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"year":"2016","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.","publist_id":"6283","date_created":"2018-12-11T11:50:06Z","citation":{"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>","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>","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>.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","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>."},"doi":"10.4230/LIPIcs.CONCUR.2016.20","_id":"1093","file_date_updated":"2018-12-12T10:11:39Z","month":"08","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","location":"Quebec City; Canada","end_date":"2016-08-26"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":501827,"relation":"main_file","access_level":"open_access","creator":"system","date_updated":"2018-12-12T10:11:39Z","date_created":"2018-12-12T10:11:39Z","file_id":"4895","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf"}],"oa_version":"Published Version","day":"01","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","first_name":"Jan"},{"first_name":"Tatjana","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","orcid":"0000-0002-9041-0905"}],"type":"conference","status":"public","alternative_title":["LIPIcs"],"intvolume":"        59","has_accepted_license":"1","scopus_import":1,"oa":1,"pubrep_id":"794","date_updated":"2023-09-07T11:58:33Z","title":"Linear distances between Markov chains","language":[{"iso":"eng"}]},{"author":[{"last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","first_name":"Harumi","full_name":"Harada, Harumi"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"}],"month":"08","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"12","oa_version":"None","status":"public","type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"article_processing_charge":"No","date_updated":"2023-09-05T14:09:01Z","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","intvolume":"      1474","language":[{"iso":"eng"}],"publication":"High-Resolution Imaging of Cellular Proteins","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":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102"}],"date_published":"2016-08-12T00:00:00Z","publisher":"Springer","quality_controlled":"1","volume":1474,"page":"203 - 216","department":[{"_id":"RySh"}],"year":"2016","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). ","publist_id":"6281","date_created":"2018-12-11T11:50:06Z","citation":{"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.","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>"},"ec_funded":1,"_id":"1094","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1007/978-1-4939-6352-2_12"},{"month":"08","conference":{"location":"Quebec City; Canada","end_date":"2016-08-26","name":"CONCUR: Concurrency Theory","start_date":"2016-08-23"},"file":[{"file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","file_id":"4795","date_created":"2018-12-12T10:10:10Z","date_updated":"2018-12-12T10:10:10Z","creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":589747}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","author":[{"last_name":"Haas","first_name":"Andreas","full_name":"Haas, Andreas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Holzer, Andreas","first_name":"Andreas","last_name":"Holzer"},{"first_name":"Christoph","full_name":"Kirsch, Christoph","last_name":"Kirsch"},{"first_name":"Michael","full_name":"Lippautz, Michael","last_name":"Lippautz"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"full_name":"Sezgin, Ali","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin"},{"last_name":"Sokolova","full_name":"Sokolova, Ana","first_name":"Ana"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"}],"type":"conference","status":"public","alternative_title":["LIPIcs"],"scopus_import":1,"has_accepted_license":"1","intvolume":"        59","date_updated":"2021-01-12T06:48:14Z","pubrep_id":"793","oa":1,"title":"Local linearizability for concurrent container-type data structures","publication":"Leibniz International Proceedings in Informatics","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["004"],"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","date_published":"2016-08-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","volume":59,"department":[{"_id":"ToHe"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"article_number":"6","ec_funded":1,"year":"2016","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).","citation":{"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>","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.","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>","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.","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>.","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>.","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."},"publist_id":"6280","date_created":"2018-12-11T11:50:07Z","doi":"10.4230/LIPIcs.CONCUR.2016.6","_id":"1095","file_date_updated":"2018-12-12T10:10:10Z"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"7186","status":"public"}]},"intvolume":"        37","scopus_import":1,"date_updated":"2023-09-07T12:56:41Z","year":"2016","issue":"6","title":"Actin rings of power","citation":{"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.","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>.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","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>","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.","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>"},"publist_id":"6279","date_created":"2018-12-11T11:50:07Z","publication":"Developmental Cell","doi":"10.1016/j.devcel.2016.05.024","language":[{"iso":"eng"}],"_id":"1096","month":"06","oa_version":"None","day":"20","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"full_name":"Schwayer, Cornelia","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer"},{"last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K"},{"full_name":"Slovakova, Jana","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova"},{"full_name":"Kardos, Roland","first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"publisher":"Cell Press","type":"journal_article","date_published":"2016-06-20T00:00:00Z","status":"public","department":[{"_id":"CaHe"}],"page":"493 - 506","quality_controlled":"1","volume":37},{"ec_funded":1,"article_number":"227","citation":{"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>","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>.","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>.","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.","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>","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.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016."},"date_created":"2018-12-11T11:50:07Z","publist_id":"6278","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. ","year":"2016","doi":"10.1145/2980179.2982427","file_date_updated":"2018-12-12T10:17:42Z","_id":"1097","abstract":[{"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.","lang":"eng"}],"ddc":["006"],"publication_status":"published","department":[{"_id":"BeBi"}],"quality_controlled":"1","volume":35,"publisher":"ACM","date_published":"2016-11-01T00:00:00Z","project":[{"call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"has_accepted_license":"1","intvolume":"        35","title":"Computational multicopter design","oa":1,"date_updated":"2021-01-12T06:48:15Z","pubrep_id":"759","issue":"6","language":[{"iso":"eng"}],"oa_version":"Submitted Version","day":"01","file":[{"file_name":"IST-2017-759-v1+1_copter.pdf","file_id":"5298","date_created":"2018-12-12T10:17:42Z","date_updated":"2018-12-12T10:17:42Z","creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":33114420}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2016-12-08","location":"Macao, China","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"month":"11","author":[{"last_name":"Du","first_name":"Tao","full_name":"Du, Tao"},{"first_name":"Adriana","full_name":"Schulz, Adriana","last_name":"Schulz"},{"first_name":"Bo","full_name":"Zhu, Bo","last_name":"Zhu"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"}],"alternative_title":["ACM Transactions on Graphics"],"status":"public","type":"conference"},{"alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","status":"public","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","first_name":"Anastasia","full_name":"Pentina, Anastasia"},{"full_name":"Urner, Ruth","first_name":"Ruth","last_name":"Urner"}],"oa_version":"Published Version","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":237111,"file_name":"IST-2017-775-v1+1_main.pdf","file_id":"4961","date_created":"2018-12-12T10:12:42Z","date_updated":"2018-12-12T10:12:42Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":185818,"creator":"system","date_updated":"2018-12-12T10:12:43Z","date_created":"2018-12-12T10:12:43Z","file_id":"4962","file_name":"IST-2017-775-v1+2_supplementary.pdf"}],"conference":{"end_date":"2016-12-10","location":"Barcelona, Spain","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"month":"12","language":[{"iso":"eng"}],"title":"Lifelong learning with weighted majority votes","pubrep_id":"775","oa":1,"date_updated":"2021-01-12T06:48:15Z","intvolume":"        29","has_accepted_license":"1","scopus_import":1,"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"page":"3619-3627","department":[{"_id":"ChLa"}],"volume":29,"quality_controlled":"1","publisher":"Neural Information Processing Systems","date_published":"2016-12-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","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."}],"ddc":["006"],"file_date_updated":"2018-12-12T10:12:43Z","_id":"1098","citation":{"chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","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.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627.","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."},"publist_id":"6277","date_created":"2018-12-11T11:50:08Z","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","year":"2016","ec_funded":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-760-v1+1_flexmolds.pdf","file_id":"4918","date_updated":"2018-12-12T10:12:01Z","date_created":"2018-12-12T10:12:01Z","creator":"system","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":11122029}],"day":"01","oa_version":"Submitted Version","month":"11","conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05","location":"Macao, China","end_date":"2016-12-08"},"author":[{"first_name":"Luigi","full_name":"Malomo, Luigi","last_name":"Malomo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"status":"public","type":"conference","alternative_title":["ACM Transactions on Graphics"],"intvolume":"        35","scopus_import":1,"has_accepted_license":"1","title":"FlexMolds: Automatic design of flexible shells for molding","issue":"6","pubrep_id":"760","oa":1,"date_updated":"2021-01-12T06:48:16Z","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"ddc":["000","005"],"publication_status":"published","quality_controlled":"1","volume":35,"department":[{"_id":"BeBi"}],"date_published":"2016-11-01T00:00:00Z","publisher":"ACM","project":[{"name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"article_number":"223","ec_funded":1,"publist_id":"6276","date_created":"2018-12-11T11:50:08Z","citation":{"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.","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>","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","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>.","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.","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>"},"year":"2016","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.","doi":"10.1145/2980179.2982397","_id":"1099","file_date_updated":"2018-12-12T10:12:01Z"},{"intvolume":"        16","has_accepted_license":"1","scopus_import":1,"pubrep_id":"754","oa":1,"date_updated":"2024-03-25T23:30:13Z","issue":"3","title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","publication":"Cell Reports","language":[{"iso":"eng"}],"month":"07","day":"19","oa_version":"Published Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":3921947,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","date_updated":"2018-12-12T10:11:04Z","date_created":"2018-12-12T10:11:04Z","file_id":"4857","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf"}],"author":[{"full_name":"Sako, Keisuke","first_name":"Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako"},{"last_name":"Pradhan","full_name":"Pradhan, Saurabh","first_name":"Saurabh"},{"orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571"},{"full_name":"Mueller, Patrick","first_name":"Patrick","last_name":"Mueller"},{"orcid":"0000-0003-4088-8633","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","full_name":"Ruprecht, Verena"},{"first_name":"Daniel","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","orcid":"0000-0001-5199-9940"},{"last_name":"Galande","full_name":"Galande, Sanjeev","first_name":"Sanjeev"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"journal_article","ec_funded":1,"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"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.","year":"2016","citation":{"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>.","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.","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>.","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>","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.","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.","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>"},"publist_id":"6275","date_created":"2018-12-11T11:50:08Z","doi":"10.1016/j.celrep.2016.06.036","file_date_updated":"2018-12-12T10:11:04Z","_id":"1100","acknowledged_ssus":[{"_id":"SSU"}],"ddc":["570","576"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","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."}],"publication_status":"published","publisher":"Cell Press","date_published":"2016-07-19T00:00:00Z","page":"866 - 877","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"volume":16,"quality_controlled":"1","project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"}]},{"publisher":"American Chemical Society","date_published":"2016-11-10T00:00:00Z","status":"public","type":"journal_article","page":"1286 - 1290","department":[{"_id":"HaJa"}],"quality_controlled":"1","volume":1,"author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L"},{"last_name":"O'Mara","full_name":"O'Mara, Megan","first_name":"Megan"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"publication_status":"published","month":"11","day":"10","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"_id":"1101","publication":"ACS SENSORS","doi":"10.1021/acssensors.6b00576","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.","date_updated":"2023-03-30T11:32:33Z","article_processing_charge":"No","year":"2016","issue":"11","date_created":"2018-12-11T11:50:09Z","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","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>","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>.","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.","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.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290."},"publist_id":"6274","scopus_import":"1","intvolume":"         1"}]