[{"publist_id":"7297","article_type":"original","volume":452,"_id":"519","day":"15","doi":"10.1016/j.jmmm.2017.12.073","month":"04","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","page":"427 - 441","department":[{"_id":"BjHo"}],"isi":1,"ddc":["530"],"scopus_import":"1","author":[{"last_name":"Altmeyer","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian","first_name":"Sebastian"}],"intvolume":"       452","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:37Z","citation":{"apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. 2018;452:427-441. doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452. Elsevier, pp. 427–441, 2018.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452, Elsevier, 2018, pp. 427–41, doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>."},"corr_author":"1","status":"public","publication_status":"published","date_published":"2018-04-15T00:00:00Z","year":"2018","language":[{"iso":"eng"}],"external_id":{"isi":["000425547700061"]},"quality_controlled":"1","date_updated":"2024-10-09T20:58:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of Magnetism and Magnetic Materials","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","date_created":"2018-12-11T11:46:56Z","publisher":"Elsevier","abstract":[{"text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ","lang":"eng"}],"file":[{"checksum":"431f5cd4a628d7ca21161f82b14ccb4f","content_type":"application/pdf","relation":"main_file","file_size":17309535,"file_name":"2018_Magnetism_Altmeyer.pdf","creator":"dernst","date_created":"2020-05-14T14:41:17Z","file_id":"7838","access_level":"open_access","date_updated":"2020-07-14T12:46:37Z"}],"oa":1},{"status":"public","publication_status":"published","date_published":"2018-10-01T00:00:00Z","year":"2018","citation":{"short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” <i>VÖB Mitteilungen</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. <a href=\"https://doi.org/10.31263/voebm.v71i1.1993\">https://doi.org/10.31263/voebm.v71i1.1993</a>.","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. <i>VÖB Mitteilungen</i>. 2018;71(1):199-206. doi:<a href=\"https://doi.org/10.31263/voebm.v71i1.1993\">10.31263/voebm.v71i1.1993</a>","apa":"Petritsch, B., &#38; Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. <i>VÖB Mitteilungen</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.31263/voebm.v71i1.1993\">https://doi.org/10.31263/voebm.v71i1.1993</a>","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” <i>VÖB Mitteilungen</i>, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” <i>VÖB Mitteilungen</i>, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:<a href=\"https://doi.org/10.31263/voebm.v71i1.1993\">10.31263/voebm.v71i1.1993</a>."},"file_date_updated":"2020-07-14T12:46:38Z","language":[{"iso":"eng"}],"issue":"1","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"        71","author":[{"last_name":"Petritsch","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"last_name":"Porsche","first_name":"Jana","full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"abstract":[{"text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.","lang":"eng"}],"file":[{"file_id":"5702","date_created":"2018-12-17T12:40:27Z","date_updated":"2020-07-14T12:46:38Z","access_level":"open_access","checksum":"7ac61bade5f37db011ca435ebcf86797","content_type":"application/pdf","relation":"main_file","file_size":509434,"file_name":"2018_VOEB_Petritsch.pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:26Z","date_created":"2018-12-11T11:44:22Z","publication":"VÖB Mitteilungen","title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","volume":71,"_id":"53","day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.31263/voebm.v71i1.1993","publist_id":"8001","ddc":["020"],"scopus_import":1,"page":"199 - 206","department":[{"_id":"E-Lib"}],"oa_version":"Published Version","month":"10","type":"journal_article"},{"date_updated":"2025-04-15T08:37:54Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:59Z","publication":"Computational Geometry: Theory and Applications","title":"Multiple covers with balls I: Inclusion–exclusion","ec_funded":1,"publisher":"Elsevier","oa":1,"file":[{"file_name":"2018_Edelsbrunner.pdf","file_size":708357,"creator":"dernst","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:38Z","date_created":"2019-02-12T06:47:52Z","file_id":"5953"}],"abstract":[{"text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.","lang":"eng"}],"intvolume":"        68","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"},{"last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel","first_name":"Mabel"}],"has_accepted_license":"1","publication_status":"published","status":"public","year":"2018","date_published":"2018-03-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:38Z","citation":{"short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. 2018;68:119-133. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” <i>Computational Geometry: Theory and Applications</i>, vol. 68. Elsevier, pp. 119–133, 2018.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>, vol. 68, Elsevier, 2018, pp. 119–33, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>."},"corr_author":"1","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000415778300010"]},"oa_version":"Preprint","month":"03","type":"journal_article","article_processing_charge":"No","ddc":["000"],"isi":1,"scopus_import":"1","page":"119 - 133","department":[{"_id":"HeEd"}],"publist_id":"7289","volume":68,"project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"_id":"530","doi":"10.1016/j.comgeo.2017.06.014","day":"01"},{"type":"journal_article","month":"10","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"CaHe"}],"page":"3 - 19","scopus_import":"1","isi":1,"publist_id":"8000","article_type":"review","_id":"54","volume":47,"day":"08","doi":"10.1016/j.devcel.2018.09.014","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-03T11:46:39Z","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","publication":"Developmental Cell","date_created":"2018-12-11T11:44:23Z","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","publisher":"Cell Press","abstract":[{"text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics.","lang":"eng"}],"oa":1,"author":[{"last_name":"Nunes Pinheiro","first_name":"Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C"},{"last_name":"Bellaïche","first_name":"Yohanns","full_name":"Bellaïche, Yohanns"}],"intvolume":"        47","issue":"1","OA_type":"free access","citation":{"short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>.","apa":"Nunes Pinheiro, D. C., &#38; Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” <i>Developmental Cell</i>, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. 2018;47(1):3-19. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>."},"date_published":"2018-10-08T00:00:00Z","year":"2018","publication_status":"published","status":"public","external_id":{"isi":["000446579900002"]},"language":[{"iso":"eng"}],"quality_controlled":"1"},{"month":"01","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","page":"186 - 191","department":[{"_id":"GaTk"}],"isi":1,"scopus_import":"1","publist_id":"7273","volume":115,"project":[{"call_identifier":"FWF","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"_id":"543","day":"02","doi":"10.1073/pnas.1711114115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/152660 ","open_access":"1"}],"date_updated":"2025-05-14T10:55:59Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Toward a unified theory of efficient, predictive, and sparse coding","date_created":"2018-12-11T11:47:04Z","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}],"oa":1,"author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper"}],"issue":"1","intvolume":"       115","citation":{"short":"M.J. Chalk, O. Marre, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 186–191.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America. 115(1), 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>."},"corr_author":"1","status":"public","publication_status":"published","year":"2018","date_published":"2018-01-02T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000419128700049"]},"quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T08:11:42Z","pubrep_id":"1066","oa_version":"Published Version","date_created":"2018-12-12T11:39:26Z","title":"Cost analysis of nondeterministic probabilistic programs","type":"technical_report","related_material":{"record":[{"status":"public","id":"6175","relation":"later_version"}]},"month":"11","publisher":"IST Austria","scopus_import":1,"oa":1,"ddc":["000"],"abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds."}],"file":[{"file_id":"5493","date_created":"2018-12-12T11:53:32Z","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","checksum":"ba3adafd36fe200385ccda583063b9eb","content_type":"application/pdf","relation":"main_file","file_name":"IST-2018-1066-v1+1_techreport.pdf","file_size":4202966,"creator":"system"},{"date_created":"2019-05-10T13:22:12Z","file_id":"6402","access_level":"closed","date_updated":"2020-07-14T12:47:00Z","content_type":"text/plain","relation":"main_file","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","creator":"dernst","file_size":322,"file_name":"authors-names.txt"}],"page":"27","author":[{"last_name":"Anonymous","full_name":"Anonymous, 1","first_name":"1"},{"full_name":"Anonymous, 2","first_name":"2","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 3","first_name":"3"},{"last_name":"Anonymous","full_name":"Anonymous, 4","first_name":"4"},{"first_name":"5","full_name":"Anonymous, 5","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"6","full_name":"Anonymous, 6"}],"has_accepted_license":"1","date_published":"2018-11-11T00:00:00Z","_id":"5457","year":"2018","publication_status":"published","status":"public","alternative_title":["IST Austria Technical Report"],"corr_author":"1","citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.","mla":"Anonymous, 1, et al. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria; 2018.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria, 2018.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, &#38; Anonymous, 6. (2018). <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria."},"file_date_updated":"2020-07-14T12:47:00Z","publication_identifier":{"issn":["2664-1690"]},"day":"11","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}],"publisher":"Elsevier","title":"Neural stem cells in neuropsychiatric disorders","publication":"Current Opinion in Neurobiology","date_created":"2018-12-11T11:47:06Z","date_updated":"2024-10-09T20:58:31Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000427101600018"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. <i>Current Opinion in Neurobiology</i>. 2018;48(2):131-138. doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>","apa":"Sacco, R., Cacci, E., &#38; Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>."},"corr_author":"1","date_published":"2018-02-01T00:00:00Z","year":"2018","status":"public","publication_status":"published","author":[{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        48","issue":"2","department":[{"_id":"GaNo"}],"page":"131 - 138","scopus_import":"1","isi":1,"article_processing_charge":"No","type":"journal_article","month":"02","oa_version":"None","day":"01","doi":"10.1016/j.conb.2017.12.005","_id":"546","volume":48,"publist_id":"7268"},{"issue":"2","intvolume":"        21","author":[{"last_name":"Gstrein","full_name":"Gstrein, Thomas","first_name":"Thomas"},{"last_name":"Edwards","full_name":"Edwards, Andrew","first_name":"Andrew"},{"full_name":"Přistoupilová, Anna","first_name":"Anna","last_name":"Přistoupilová"},{"last_name":"Leca","full_name":"Leca, Ines","first_name":"Ines"},{"full_name":"Breuss, Martin","first_name":"Martin","last_name":"Breuss"},{"first_name":"Sandra","full_name":"Pilat Carotta, Sandra","last_name":"Pilat Carotta"},{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"last_name":"Tripathy","full_name":"Tripathy, Ratna","first_name":"Ratna"},{"last_name":"Traunbauer","full_name":"Traunbauer, Anna","first_name":"Anna"},{"full_name":"Hochstoeger, Tobias","first_name":"Tobias","last_name":"Hochstoeger"},{"last_name":"Rosoklija","first_name":"Gavril","full_name":"Rosoklija, Gavril"},{"last_name":"Repic","first_name":"Marco","full_name":"Repic, Marco"},{"last_name":"Landler","full_name":"Landler, Lukas","first_name":"Lukas"},{"last_name":"Stránecký","first_name":"Viktor","full_name":"Stránecký, Viktor"},{"full_name":"Dürnberger, Gerhard","first_name":"Gerhard","last_name":"Dürnberger"},{"last_name":"Keane","first_name":"Thomas","full_name":"Keane, Thomas"},{"last_name":"Zuber","first_name":"Johannes","full_name":"Zuber, Johannes"},{"last_name":"Adams","full_name":"Adams, David","first_name":"David"},{"last_name":"Flint","full_name":"Flint, Jonathan","first_name":"Jonathan"},{"last_name":"Honzik","first_name":"Tomas","full_name":"Honzik, Tomas"},{"last_name":"Gut","full_name":"Gut, Marta","first_name":"Marta"},{"first_name":"Sergi","full_name":"Beltran, Sergi","last_name":"Beltran"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"full_name":"Sherr, Elliott","first_name":"Elliott","last_name":"Sherr"},{"full_name":"Kmoch, Stanislav","first_name":"Stanislav","last_name":"Kmoch"},{"first_name":"Ivo","full_name":"Gut, Ivo","last_name":"Gut"},{"full_name":"Keays, David","first_name":"David","last_name":"Keays"}],"publist_id":"7267","publication_status":"published","volume":21,"status":"public","extern":"1","date_published":"2018-06-06T00:00:00Z","_id":"547","year":"2018","citation":{"short":"T. Gstrein, A. Edwards, A. Přistoupilová, I. Leca, M. Breuss, S. Pilat Carotta, A.H. Hansen, R. Tripathy, A. Traunbauer, T. Hochstoeger, G. Rosoklija, M. Repic, L. Landler, V. Stránecký, G. Dürnberger, T. Keane, J. Zuber, D. Adams, J. Flint, T. Honzik, M. Gut, S. Beltran, K. Mechtler, E. Sherr, S. Kmoch, I. Gut, D. Keays, Nature Neuroscience 21 (2018) 207–217.","chicago":"Gstrein, Thomas, Andrew Edwards, Anna Přistoupilová, Ines Leca, Martin Breuss, Sandra Pilat Carotta, Andi H Hansen, et al. “Mutations in Vps15 Perturb Neuronal Migration in Mice and Are Associated with Neurodevelopmental Disease in Humans.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41593-017-0053-5\">https://doi.org/10.1038/s41593-017-0053-5</a>.","ista":"Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat Carotta S, Hansen AH, Tripathy R, Traunbauer A, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, Keane T, Zuber J, Adams D, Flint J, Honzik T, Gut M, Beltran S, Mechtler K, Sherr E, Kmoch S, Gut I, Keays D. 2018. Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. Nature Neuroscience. 21(2), 207–217.","ama":"Gstrein T, Edwards A, Přistoupilová A, et al. Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. <i>Nature Neuroscience</i>. 2018;21(2):207-217. doi:<a href=\"https://doi.org/10.1038/s41593-017-0053-5\">10.1038/s41593-017-0053-5</a>","apa":"Gstrein, T., Edwards, A., Přistoupilová, A., Leca, I., Breuss, M., Pilat Carotta, S., … Keays, D. (2018). Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41593-017-0053-5\">https://doi.org/10.1038/s41593-017-0053-5</a>","ieee":"T. Gstrein <i>et al.</i>, “Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans,” <i>Nature Neuroscience</i>, vol. 21, no. 2. Nature Publishing Group, pp. 207–217, 2018.","mla":"Gstrein, Thomas, et al. “Mutations in Vps15 Perturb Neuronal Migration in Mice and Are Associated with Neurodevelopmental Disease in Humans.” <i>Nature Neuroscience</i>, vol. 21, no. 2, Nature Publishing Group, 2018, pp. 207–17, doi:<a href=\"https://doi.org/10.1038/s41593-017-0053-5\">10.1038/s41593-017-0053-5</a>."},"language":[{"iso":"eng"}],"external_id":{"isi":["000424269900012"]},"doi":"10.1038/s41593-017-0053-5","day":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T08:59:52Z","acknowledgement":"We also acknowledge the input of P. Potter and S. Wells from the mutagenesis program at MRC Harwell and the MRC funding that underpinned it (MC U142684172). We are indebted to R. Williams for modeling the VPS15 human mutation. We also thank the transgenic, bio-optics, proteomic and graphics services groups at the IMP/IMBA. We thank The National Center for Medical Genomics (LM2015091) for providing allelic frequencies in ethnically matched populations (project CZ.02.1.01/0.0/0.0/16_013/0001634). We thank Boehringer Ingelheim and the FWF for funding this research (D.A.K., I914, P24267). The human studies were funded by the European Community’s 7th Framework Program (FP7/2007-2013). S.K., A.P. and V.S. were supported by institutional programs of Charles University in Prague (UNCE 204011, PROGRES-Q26/LF1 and SVV 260367/2017). We acknowledge grants 15-28208A and RVO-VFN 64165 from the Ministry of Health of the Czech Republic and the project LQ1604 NPU II from the Ministry of Education.","date_created":"2018-12-11T11:47:06Z","oa_version":"None","month":"06","publication":"Nature Neuroscience","title":"Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans","type":"journal_article","article_processing_charge":"No","publisher":"Nature Publishing Group","isi":1,"page":"207 - 217","abstract":[{"text":"The formation of the vertebrate brain requires the generation, migration, differentiation and survival of neurons. Genetic mutations that perturb these critical cellular events can result in malformations of the telencephalon, providing a molecular window into brain development. Here we report the identification of an N-ethyl-N-nitrosourea-induced mouse mutant characterized by a fractured hippocampal pyramidal cell layer, attributable to defects in neuronal migration. We show that this is caused by a hypomorphic mutation in Vps15 that perturbs endosomal-lysosomal trafficking and autophagy, resulting in an upregulation of Nischarin, which inhibits Pak1 signaling. The complete ablation of Vps15 results in the accumulation of autophagic substrates, the induction of apoptosis and severe cortical atrophy. Finally, we report that mutations in VPS15 are associated with cortical atrophy and epilepsy in humans. These data highlight the importance of the Vps15-Vps34 complex and the Nischarin-Pak1 signaling hub in the development of the telencephalon.","lang":"eng"}]},{"oa_version":"Published Version","type":"journal_article","month":"10","article_processing_charge":"No","scopus_import":"1","isi":1,"department":[{"_id":"SyCr"}],"page":"R1139 - R1140","publist_id":"7999","article_type":"original","_id":"55","volume":28,"day":"08","doi":"10.1016/j.cub.2018.08.063","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-15T12:06:46Z","date_created":"2018-12-11T11:44:23Z","title":"Protection against the lethal side effects of social immunity in ants","publication":"Current Biology","publisher":"Cell Press","oa":1,"abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"intvolume":"        28","issue":"19","author":[{"last_name":"Pull","full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher"},{"last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494"},{"last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth"},{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"year":"2018","date_published":"2018-10-08T00:00:00Z","publication_status":"published","status":"public","citation":{"short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","apa":"Pull, C., Metzler, S., Naderlinger, E., &#38; Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” <i>Current Biology</i>, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. 2018;28(19):R1139-R1140. doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000446693400008"]}},{"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:52:52Z","date_created":"2018-12-11T11:47:09Z","title":"The Bogoliubov free energy functional II: The dilute Limit","publication":"Communications in Mathematical Physics","publisher":"Springer","oa":1,"abstract":[{"lang":"eng","text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.)."}],"intvolume":"       360","issue":"1","author":[{"last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M"},{"last_name":"Reuvers","full_name":"Reuvers, Robin","first_name":"Robin"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"year":"2018","date_published":"2018-05-01T00:00:00Z","publication_status":"published","status":"public","citation":{"ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1. Springer, pp. 347–403, 2018.","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. 2018;360(1):347-403. doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>."},"quality_controlled":"1","external_id":{"arxiv":["1511.05953"]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","type":"journal_article","month":"05","article_processing_charge":"No","scopus_import":"1","department":[{"_id":"RoSe"}],"page":"347-403","publist_id":"7260","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"_id":"554","volume":360,"publication_identifier":{"issn":["0010-3616"]},"day":"01","doi":"10.1007/s00220-017-3064-x"},{"author":[{"last_name":"Richter","full_name":"Richter, Ralf","first_name":"Ralf"},{"first_name":"Natalia","full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova"},{"first_name":"Anthony","full_name":"Day, Anthony","last_name":"Day"},{"full_name":"Kwok, Jessica","first_name":"Jessica","last_name":"Kwok"}],"intvolume":"        50","citation":{"chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>, vol. 50, Elsevier, 2018, pp. 65–74, doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018.","apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74."},"publication_status":"published","status":"public","date_published":"2018-06-01T00:00:00Z","year":"2018","external_id":{"isi":["000443661300011"]},"language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T14:07:03Z","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/125524/"}],"publication":"Current Opinion in Structural Biology","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","date_created":"2018-12-11T11:47:09Z","publisher":"Elsevier","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"oa":1,"publist_id":"7259","article_type":"original","volume":50,"_id":"555","doi":"10.1016/j.sbi.2017.12.002","day":"01","month":"06","type":"journal_article","oa_version":"Submitted Version","article_processing_charge":"No","page":"65 - 74","department":[{"_id":"MaLo"}],"isi":1,"scopus_import":"1"},{"date_created":"2018-12-11T11:47:09Z","title":"The free boundary Schur process and applications I","publication":"Annales Henri Poincare","arxiv":1,"date_updated":"2025-09-18T07:34:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"file":[{"file_name":"2018_Annales_Betea.pdf","file_size":3084674,"creator":"dernst","checksum":"0c38abe73569b7166b7487ad5d23cc68","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:03Z","file_id":"5866","date_created":"2019-01-21T15:18:55Z"}],"abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"ec_funded":1,"publisher":"Springer Nature","has_accepted_license":"1","intvolume":"        19","issue":"12","author":[{"full_name":"Betea, Dan","first_name":"Dan","last_name":"Betea"},{"last_name":"Bouttier","full_name":"Bouttier, Jeremie","first_name":"Jeremie"},{"full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar"},{"last_name":"Vuletic","full_name":"Vuletic, Mirjana","first_name":"Mirjana"}],"quality_controlled":"1","external_id":{"arxiv":["1704.05809"],"isi":["000450487900003"]},"language":[{"iso":"eng"}],"date_published":"2018-11-13T00:00:00Z","year":"2018","publication_status":"published","status":"public","citation":{"apa":"Betea, D., Bouttier, J., Nejjar, P., &#38; Vuletic, M. (2018). The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” <i>Annales Henri Poincare</i>, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. 2018;19(12):3663-3742. doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>."},"file_date_updated":"2020-07-14T12:47:03Z","oa_version":"Published Version","type":"journal_article","month":"11","scopus_import":"1","ddc":["500"],"isi":1,"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"page":"3663-3742","article_processing_charge":"Yes (via OA deal)","article_type":"original","publist_id":"7258","publication_identifier":{"issn":["1424-0637"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"13","doi":"10.1007/s00023-018-0723-1","_id":"556","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"volume":19},{"title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","datarep_id":"82","type":"research_data","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"keyword":["graph matching","quadratic assignment problem<"],"month":"01","oa_version":"Published Version","date_created":"2018-12-12T12:31:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:41:17Z","abstract":[{"text":"Graph matching problems for large displacement optical flow of RGB-D images.","lang":"eng"}],"department":[{"_id":"VlKo"}],"file":[{"date_updated":"2020-07-14T12:47:05Z","access_level":"open_access","date_created":"2018-12-12T13:02:34Z","file_id":"5600","creator":"system","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","file_size":1737958,"content_type":"application/zip","relation":"main_file","checksum":"53c17082848e12f3c2e1b4185b578208"}],"oa":1,"ddc":["001"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","has_accepted_license":"1","contributor":[{"contributor_type":"researcher","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"}],"author":[{"full_name":"Alhaija, Hassan","first_name":"Hassan","last_name":"Alhaija"},{"full_name":"Sellent, Anita","first_name":"Anita","last_name":"Sellent"},{"last_name":"Kondermann","full_name":"Kondermann, Daniel","first_name":"Daniel"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"04","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"doi":"10.15479/AT:ISTA:82","file_date_updated":"2020-07-14T12:47:05Z","citation":{"chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:82\">https://doi.org/10.15479/AT:ISTA:82</a>.","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","mla":"Alhaija, Hassan, et al. <i>Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>.","ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>.","apa":"Alhaija, H., Sellent, A., Kondermann, D., &#38; Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:82\">https://doi.org/10.15479/AT:ISTA:82</a>","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018."},"year":"2018","_id":"5573","date_published":"2018-01-04T00:00:00Z","status":"public"},{"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis"}],"has_accepted_license":"1","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"citation":{"mla":"Ellis, Thomas. <i>Data and Python Scripts Supporting Python Package FAPS</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>.","short":"T. Ellis, (2018)."},"file_date_updated":"2020-07-14T12:47:07Z","status":"public","date_published":"2018-02-12T00:00:00Z","_id":"5583","year":"2018","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"day":"12","doi":"10.15479/AT:ISTA:95","date_updated":"2025-04-15T07:11:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","related_material":{"record":[{"id":"286","relation":"research_paper","status":"public"}]},"title":"Data and Python scripts supporting Python package FAPS","type":"research_data","datarep_id":"95","oa_version":"Published Version","date_created":"2018-12-12T12:31:39Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"file":[{"relation":"main_file","content_type":"text/csv","checksum":"fc6aab51439f2622ba6df8632e66fd4f","creator":"system","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","file_size":122048,"date_created":"2018-12-12T13:02:41Z","file_id":"5606","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z"},{"checksum":"92347586ae4f8a6eb7c04354797bf314","content_type":"text/csv","relation":"main_file","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","file_size":235980,"creator":"system","date_created":"2018-12-12T13:02:42Z","file_id":"5607","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","file_id":"5608","date_created":"2018-12-12T13:02:43Z","creator":"system","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","file_size":311712,"content_type":"text/csv","relation":"main_file","checksum":"3300813645a54e6c5c39f41917228354"},{"creator":"system","file_size":342090,"file_name":"IST-2018-95-v1+4_faps_scripts.zip","content_type":"application/zip","relation":"main_file","checksum":"e739fc473567fd8f39438b445fc46147","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z","file_id":"5609","date_created":"2018-12-12T13:02:44Z"}],"department":[{"_id":"NiBa"}],"oa":1},{"oa":1,"ddc":["570"],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. 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Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., &#38; Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","mla":"Deny, Stephane, et al. <i>Nonlinear Decoding of a Complex Movie from the Mammalian Retina</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>."},"file_date_updated":"2020-07-14T12:47:07Z","has_accepted_license":"1","author":[{"full_name":"Deny, Stephane","first_name":"Stephane","last_name":"Deny"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Vicente","full_name":"Botella-Soler, Vicente","last_name":"Botella-Soler"},{"last_name":"Martius","first_name":"Georg S","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}]},{"has_accepted_license":"1","contributor":[{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard"}],"author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"doi":"10.15479/AT:ISTA:109","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"day":"24","file_date_updated":"2020-07-14T12:47:08Z","citation":{"ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","mla":"Vicoso, Beatriz. <i>Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018)</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","short":"B. Vicoso, (2018).","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>."},"_id":"5586","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF"}],"year":"2018","date_published":"2018-07-24T00:00:00Z","status":"public","type":"research_data","title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","datarep_id":"109","month":"07","related_material":{"record":[{"status":"public","id":"131","relation":"research_paper"}]},"keyword":["schistosoma","Z-chromosome","gene expression"],"date_created":"2018-12-12T12:31:40Z","oa_version":"Published Version","date_updated":"2025-04-15T08:18:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:08Z","access_level":"open_access","date_created":"2018-12-12T13:02:35Z","file_id":"5601","creator":"system","file_size":11918144,"file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","relation":"main_file","content_type":"application/zip","checksum":"e60b484bd6f55c08eb66a189cb72c923"}],"ddc":["570"],"oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No"},{"has_accepted_license":"1","author":[{"first_name":"Daniele","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"doi":"10.15479/AT:ISTA:62","day":"21","file_date_updated":"2020-07-14T12:47:08Z","citation":{"short":"D. De Martino, G. Tkačik, (2018).","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>.","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>","apa":"De Martino, D., &#38; Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","mla":"De Martino, Daniele, and Gašper Tkačik. <i>Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>."},"status":"public","year":"2018","_id":"5587","date_published":"2018-09-21T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"month":"09","related_material":{"record":[{"status":"public","id":"161","relation":"research_paper"}]},"keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"datarep_id":"111","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","type":"research_data","date_created":"2018-12-12T12:31:41Z","oa_version":"Published Version","date_updated":"2025-04-15T06:50:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra  (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and  \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"file":[{"checksum":"97992e3e8cf8544ec985a48971708726","content_type":"application/zip","relation":"main_file","file_size":14376,"file_name":"IST-2018-111-v1+1_CODES.zip","creator":"system","file_id":"5641","date_created":"2018-12-12T13:05:13Z","access_level":"open_access","date_updated":"2020-07-14T12:47:08Z"}],"department":[{"_id":"GaTk"}],"ddc":["530"],"oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","ec_funded":1},{"has_accepted_license":"1","author":[{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:0113","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"day":"07","citation":{"chicago":"Hauschild, Robert. “Fluorescence Lifetime Analysis of FLIM X16 TCSPC Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">https://doi.org/10.15479/AT:ISTA:0113</a>.","short":"R. Hauschild, (2018).","mla":"Hauschild, Robert. <i>Fluorescence Lifetime Analysis of FLIM X16 TCSPC Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>.","apa":"Hauschild, R. (2018). Fluorescence lifetime analysis of FLIM X16 TCSPC data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">https://doi.org/10.15479/AT:ISTA:0113</a>","ieee":"R. Hauschild, “Fluorescence lifetime analysis of FLIM X16 TCSPC data.” Institute of Science and Technology Austria, 2018.","ama":"Hauschild R. Fluorescence lifetime analysis of FLIM X16 TCSPC data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>","ista":"Hauschild R. 2018. Fluorescence lifetime analysis of FLIM X16 TCSPC data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>."},"file_date_updated":"2020-07-14T12:47:08Z","_id":"5588","date_published":"2018-11-07T00:00:00Z","year":"2018","status":"public","type":"research_data","title":"Fluorescence lifetime analysis of FLIM X16 TCSPC data","datarep_id":"113","keyword":["FLIM","FRET","fluorescence lifetime imaging"],"month":"11","date_created":"2018-12-12T12:31:41Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:44:21Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:08Z","date_created":"2019-04-11T18:15:01Z","file_id":"6296","creator":"rhauschild","file_name":"IST-2018-113-v1+1_FLIMX16TCSPCLifeTimeFit.zip","file_size":47866557,"relation":"main_file","content_type":"application/x-zip-compressed","checksum":"a4e160054c9114600624cf89a925fd7d"}],"department":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data)"}],"oa":1,"ddc":["570"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No"},{"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","creator":"dernst","file_size":787407,"file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","file_id":"7046","date_created":"2019-11-19T07:47:43Z","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z"}],"abstract":[{"text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}],"oa":1,"publisher":"Springer","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","publication":"Neurotrophic Factors","date_created":"2018-12-11T11:47:11Z","pmid":1,"date_updated":"2021-01-12T08:03:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"external_id":{"pmid":["29222783"]},"quality_controlled":"1","citation":{"short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in <i>Neurotrophic Factors</i>, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. <i>Neurotrophic Factors</i>. Vol 1727. Springer; 2018:201-215. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., &#38; Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), <i>Neurotrophic Factors</i> (Vol. 1727, pp. 201–215). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>."},"alternative_title":["Methods in Molecular Biology"],"file_date_updated":"2020-07-14T12:47:09Z","date_published":"2018-01-01T00:00:00Z","year":"2018","status":"public","publication_status":"published","has_accepted_license":"1","author":[{"last_name":"Dimitrov","full_name":"Dimitrov, Dimitar","first_name":"Dimitar"},{"first_name":"Laurent","full_name":"Guillaud, Laurent","last_name":"Guillaud"},{"first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"intvolume":"      1727","department":[{"_id":"RySh"}],"page":"201 - 215","scopus_import":1,"ddc":["570"],"editor":[{"last_name":"Skaper","first_name":"Stephen D.","full_name":"Skaper, Stephen D."}],"article_processing_charge":"No","type":"book_chapter","month":"01","oa_version":"Submitted Version","doi":"10.1007/978-1-4939-7571-6_15","day":"01","_id":"562","volume":1727,"publist_id":"7252"},{"ec_funded":1,"publisher":"Academic Press","oa":1,"file":[{"file_name":"bartonetheridge.pdf","file_size":2287682,"creator":"nbarton","checksum":"0b96f6db47e3e91b5e7d103b847c239d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","file_id":"7199"}],"abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-04-15T07:11:04Z","date_created":"2018-12-11T11:47:12Z","title":"Establishment in a new habitat by polygenic adaptation","related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"publication":"Theoretical Population Biology","date_published":"2018-07-01T00:00:00Z","year":"2018","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:47:09Z","citation":{"mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” <i>Theoretical Population Biology</i>, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. 2018;122(7):110-127. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>","apa":"Barton, N. H., &#38; Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>. Academic Press, 2018. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127."},"quality_controlled":"1","external_id":{"isi":["000440392900014"]},"language":[{"iso":"eng"}],"intvolume":"       122","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"7","author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","ddc":["519","576"],"isi":1,"department":[{"_id":"NiBa"}],"page":"110-127","oa_version":"Submitted Version","type":"journal_article","month":"07","_id":"564","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"volume":122,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"day":"01","doi":"10.1016/j.tpb.2017.11.007","publist_id":"7250","article_type":"original"}]