[{"article_processing_charge":"No","department":[{"_id":"RoSe"}],"publist_id":"8002","language":[{"iso":"eng"}],"pubrep_id":"1043","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser"}],"title":"Point interactions in systems of fermions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"6256","content_type":"application/pdf","file_size":851164,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"fbd8c747d148b468a21213b7cf175225","file_name":"2018_Thesis_Moser.pdf","date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z"},{"checksum":"c28e16ecfc1126d3ce324ec96493c01e","relation":"source_file","access_level":"closed","creator":"dernst","file_size":1531516,"file_id":"6257","content_type":"application/zip","date_created":"2019-04-09T07:45:38Z","date_updated":"2020-07-14T12:46:37Z","file_name":"2018_Thesis_Moser_Source.zip"}],"project":[{"call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"publication_status":"published","citation":{"mla":"Moser, Thomas. <i>Point Interactions in Systems of Fermions</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">10.15479/AT:ISTA:th_1043</a>.","apa":"Moser, T. (2018). <i>Point interactions in systems of fermions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">https://doi.org/10.15479/AT:ISTA:th_1043</a>","chicago":"Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">https://doi.org/10.15479/AT:ISTA:th_1043</a>.","ieee":"T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018.","short":"T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018.","ista":"Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria.","ama":"Moser T. Point interactions in systems of fermions. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1043\">10.15479/AT:ISTA:th_1043</a>"},"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:37Z","type":"dissertation","_id":"52","page":"115","year":"2018","alternative_title":["ISTA Thesis"],"date_published":"2018-09-04T00:00:00Z","month":"09","date_updated":"2023-09-27T12:34:14Z","oa":1,"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_1043","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5856"},{"relation":"part_of_dissertation","status":"public","id":"154"},{"id":"1198","status":"public","relation":"part_of_dissertation"},{"id":"741","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","date_created":"2018-12-11T11:44:22Z","ddc":["515","530","519"],"day":"04","status":"public","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}]},{"language":[{"iso":"eng"}],"publist_id":"8001","department":[{"_id":"E-Lib"}],"file":[{"content_type":"application/pdf","file_id":"5702","file_size":509434,"creator":"dernst","checksum":"7ac61bade5f37db011ca435ebcf86797","access_level":"open_access","relation":"main_file","file_name":"2018_VOEB_Petritsch.pdf","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-17T12:40:27Z"}],"title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","author":[{"last_name":"Petritsch","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Petritsch, Barbara"},{"id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Porsche","full_name":"Porsche, Jana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","has_accepted_license":"1","publication_status":"published","_id":"53","file_date_updated":"2020-07-14T12:46:38Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"scopus_import":1,"citation":{"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>","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>.","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>","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.","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","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>."},"year":"2018","license":"https://creativecommons.org/licenses/by/4.0/","page":"199 - 206","issue":"1","oa":1,"date_updated":"2021-01-12T08:01:26Z","month":"10","intvolume":"        71","date_published":"2018-10-01T00:00:00Z","oa_version":"Published Version","doi":"10.31263/voebm.v71i1.1993","publication":"VÖB Mitteilungen","status":"public","day":"01","date_created":"2018-12-11T11:44:22Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["020"],"volume":71},{"oa":1,"date_updated":"2023-09-13T08:59:00Z","month":"03","intvolume":"        68","date_published":"2018-03-01T00:00:00Z","year":"2018","external_id":{"isi":["000415778300010"]},"page":"119 - 133","status":"public","day":"01","date_created":"2018-12-11T11:46:59Z","ddc":["000"],"volume":68,"isi":1,"ec_funded":1,"oa_version":"Preprint","doi":"10.1016/j.comgeo.2017.06.014","publication":"Computational Geometry: Theory and Applications","file":[{"file_size":708357,"creator":"dernst","file_id":"5953","content_type":"application/pdf","relation":"main_file","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","access_level":"open_access","file_name":"2018_Edelsbrunner.pdf","date_created":"2019-02-12T06:47:52Z","date_updated":"2020-07-14T12:46:38Z"}],"title":"Multiple covers with balls I: Inclusion–exclusion","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7289","department":[{"_id":"HeEd"}],"article_processing_charge":"No","quality_controlled":"1","_id":"530","type":"journal_article","file_date_updated":"2020-07-14T12:46:38Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"citation":{"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>","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>.","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.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 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>."},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}]},{"oa":1,"issue":"6","date_updated":"2023-02-23T12:23:25Z","date_published":"2018-11-01T00:00:00Z","month":"11","intvolume":"        31","year":"2018","page":"489-501","day":"01","status":"public","ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:01Z","volume":31,"oa_version":"Published Version","publication":"Distributed Computing","doi":"10.1007/s00446-017-0315-1","title":"Communication-efficient randomized consensus","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"last_name":"King","first_name":"Valerie","full_name":"King, Valerie"},{"last_name":"Saia","first_name":"Jared","full_name":"Saia, Jared"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:38Z","date_created":"2019-01-22T07:25:51Z","file_name":"2017_DistribComp_Alistarh.pdf","access_level":"open_access","relation":"main_file","checksum":"69b46e537acdcac745237ddb853fcbb5","creator":"dernst","file_size":595707,"content_type":"application/pdf","file_id":"5867"}],"publisher":"Springer","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7281","department":[{"_id":"DaAl"}],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"536","scopus_import":1,"abstract":[{"text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:46:38Z","citation":{"apa":"Alistarh, D.-A., Aspnes, J., King, V., &#38; Saia, J. (2018). Communication-efficient randomized consensus. <i>Distributed Computing</i>. Springer. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” <i>Distributed Computing</i>, vol. 31, no. 6. Springer, pp. 489–501, 2018.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. <i>Distributed Computing</i>. 2018;31(6):489-501. doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>."},"publication_identifier":{"issn":["01782770"]},"publication_status":"published","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"doi":"10.15479/AT:ISTA:th_930","degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1024"}]},"day":"01","status":"public","supervisor":[{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:03Z","ddc":["570"],"page":"147","year":"2018","alternative_title":["ISTA Thesis"],"date_published":"2018-01-01T00:00:00Z","month":"01","oa":1,"date_updated":"2023-09-07T12:41:06Z","publication_status":"published","abstract":[{"lang":"eng","text":"The whole life cycle of plants as well as their responses to environmental stimuli is governed by a complex network of hormonal regulations. A number of studies have demonstrated an essential role of both auxin and cytokinin in the regulation of many aspects of plant growth and development including embryogenesis, postembryonic organogenic processes such as root, and shoot branching, root and shoot apical meristem activity and phyllotaxis. Over the last decades essential knowledge on the key molecular factors and pathways that spatio-temporally define auxin and cytokinin activities in the plant body has accumulated. However, how both hormonal pathways are interconnected by a complex network of interactions and feedback circuits that determines the final outcome of the individual hormone actions is still largely unknown. Root system architecture establishment and in particular formation of lateral organs is prime example of developmental process at whose regulation both auxin and cytokinin pathways converge. To dissect convergence points and pathways that tightly balance auxin - cytokinin antagonistic activities that determine the root branching pattern transcriptome profiling was applied. Genome wide expression analyses of the xylem pole pericycle, a tissue giving rise to lateral roots, led to identification of genes that are highly responsive to combinatorial auxin and cytokinin treatments and play an essential function in the auxin-cytokinin regulated root branching. SYNERGISTIC AUXIN CYTOKININ 1 (SYAC1) gene, which encodes for a protein of unknown function, was detected among the top candidate genes of which expression was synergistically up-regulated by simultaneous hormonal treatment. Plants with modulated SYAC1 activity exhibit severe defects in the root system establishment and attenuate developmental responses to both auxin and cytokinin. To explore the biological function of the SYAC1, we employed different strategies including expression pattern analysis, subcellular localization and phenotypic analyses of the syac1 loss-of-function and gain-of-function transgenic lines along with the identification of the SYAC1 interaction partners. Detailed functional characterization revealed that SYAC1 acts as a developmentally specific regulator of the secretory pathway to control deposition of cell wall components and thereby rapidly fine tune elongation growth."}],"file_date_updated":"2020-12-02T23:30:08Z","type":"dissertation","citation":{"mla":"Hurny, Andrej. <i>Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>.","apa":"Hurny, A. (2018). <i>Identification and characterization of novel auxin-cytokinin cross-talk components</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>","chicago":"Hurny, Andrej. “Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">https://doi.org/10.15479/AT:ISTA:th_930</a>.","ieee":"A. Hurny, “Identification and characterization of novel auxin-cytokinin cross-talk components,” Institute of Science and Technology Austria, 2018.","short":"A. Hurny, Identification and Characterization of Novel Auxin-Cytokinin Cross-Talk Components, Institute of Science and Technology Austria, 2018.","ista":"Hurny A. 2018. Identification and characterization of novel auxin-cytokinin cross-talk components. Institute of Science and Technology Austria.","ama":"Hurny A. Identification and characterization of novel auxin-cytokinin cross-talk components. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_930\">10.15479/AT:ISTA:th_930</a>"},"publication_identifier":{"issn":["2663-337X"]},"_id":"539","publist_id":"7277","department":[{"_id":"EvBe"}],"article_processing_charge":"No","pubrep_id":"930","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"Identification and characterization of novel auxin-cytokinin cross-talk components","author":[{"first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426","last_name":"Hurny","full_name":"Hurny, Andrej"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2018_Hurny_thesis_source.docx","date_updated":"2020-12-02T23:30:08Z","date_created":"2019-04-05T09:37:56Z","embargo_to":"open_access","file_size":28112114,"creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6226","relation":"source_file","checksum":"0c9d6d1c80d9857e6e545213467bbcb2","access_level":"closed"},{"file_id":"6227","content_type":"application/pdf","file_size":12524427,"creator":"dernst","access_level":"open_access","checksum":"ecbe481a1413d270bd501b872c7ed54f","relation":"main_file","embargo":"2019-07-10","file_name":"2018_Hurny_thesis.pdf","date_created":"2019-04-05T09:37:55Z","date_updated":"2020-12-02T09:52:16Z"}]},{"article_processing_charge":"No","department":[{"_id":"CaHe"}],"publist_id":"8000","language":[{"iso":"eng"}],"article_type":"review","publisher":"Cell Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","author":[{"full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C"},{"full_name":"Bellaïche, Yohanns","first_name":"Yohanns","last_name":"Bellaïche"}],"publication_status":"published","citation":{"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>.","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>","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>.","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","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>"},"type":"journal_article","scopus_import":"1","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"}],"_id":"54","quality_controlled":"1","external_id":{"isi":["000446579900002"]},"page":"3 - 19","year":"2018","intvolume":"        47","month":"10","date_published":"2018-10-08T00:00:00Z","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.","date_updated":"2023-09-13T08:54:38Z","issue":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"doi":"10.1016/j.devcel.2018.09.014","publication":"Developmental Cell","isi":1,"oa_version":"Published Version","volume":47,"date_created":"2018-12-11T11:44:23Z","status":"public","day":"08"},{"date_published":"2018-01-01T00:00:00Z","intvolume":"       208","month":"01","date_updated":"2024-02-21T13:48:27Z","oa":1,"issue":"1","page":"365 - 375","external_id":{"isi":["000419356300024"]},"year":"2018","volume":208,"date_created":"2018-12-11T11:47:04Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"day":"01","status":"public","publication":"Genetics","doi":"10.1534/genetics.117.300513","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5571"},{"id":"5572","relation":"popular_science","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","isi":1,"has_accepted_license":"1","publisher":"Genetics Society of America","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"file":[{"file_size":1311661,"creator":"system","content_type":"application/pdf","file_id":"5132","relation":"main_file","access_level":"open_access","checksum":"2123845e7031a0cf043905be160f9e69","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_created":"2018-12-12T10:15:14Z","date_updated":"2020-07-14T12:46:50Z"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"publist_id":"7274","language":[{"iso":"eng"}],"article_type":"original","pubrep_id":"1058","citation":{"ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. 2018;208(1):365-375. doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>.","apa":"Kelemen, R. K., &#38; Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>."},"abstract":[{"lang":"eng","text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:46:50Z","_id":"542","quality_controlled":"1","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"publication_status":"published"},{"publisher":"National Academy of Sciences","title":"Toward a unified theory of efficient, predictive, and sparse coding","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"publist_id":"7273","language":[{"iso":"eng"}],"citation":{"apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>PNAS</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>.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>PNAS</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>PNAS</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>."},"type":"journal_article","scopus_import":"1","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."}],"_id":"543","quality_controlled":"1","project":[{"grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes"}],"publication_status":"published","month":"01","intvolume":"       115","date_published":"2018-01-02T00:00:00Z","date_updated":"2023-09-19T10:16:35Z","issue":"1","oa":1,"page":"186 - 191","external_id":{"isi":["000419128700049"]},"year":"2018","volume":115,"date_created":"2018-12-11T11:47:04Z","day":"02","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"doi":"10.1073/pnas.1711114115","publication":"PNAS","isi":1,"oa_version":"Submitted Version"},{"quality_controlled":"1","_id":"544","type":"journal_article","file_date_updated":"2020-07-14T12:46:56Z","scopus_import":"1","abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"citation":{"chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>.","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. 2018;8(3):845-857. doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.","ieee":"A. György <i>et al.</i>, “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>"},"publication_status":"published","project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF"},{"grant_number":"P29638","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"_id":"2637E9C0-B435-11E9-9278-68D0E5697425","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis","grant_number":"LSC16-021 "},{"grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":2251222,"creator":"system","content_type":"application/pdf","file_id":"4905","checksum":"7d9d28b915159078a4ca7add568010e8","relation":"main_file","access_level":"open_access","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","date_updated":"2020-07-14T12:46:56Z","date_created":"2018-12-12T10:11:48Z"}],"author":[{"last_name":"György","orcid":"0000-0002-1819-198X","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila"},{"orcid":"0000-0001-9588-1389","last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","full_name":"Roblek, Marko"},{"last_name":"Ratheesh","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna","full_name":"Ratheesh, Aparna"},{"last_name":"Valosková","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","full_name":"Valosková, Katarina"},{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","last_name":"Belyaeva","full_name":"Belyaeva, Vera"},{"full_name":"Wachner, Stephanie","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner"},{"last_name":"Matsubayashi","first_name":"Yutaka","full_name":"Matsubayashi, Yutaka"},{"full_name":"Sanchez Sanchez, Besaiz","last_name":"Sanchez Sanchez","first_name":"Besaiz"},{"first_name":"Brian","last_name":"Stramer","full_name":"Stramer, Brian"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","publisher":"Genetics Society of America","has_accepted_license":"1","pubrep_id":"990","language":[{"iso":"eng"}],"publist_id":"7271","department":[{"_id":"DaSi"}],"article_processing_charge":"No","status":"public","day":"01","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:05Z","volume":8,"isi":1,"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"relation":"research_paper","id":"6530"},{"id":"6543","relation":"research_paper"},{"relation":"dissertation_contains","status":"public","id":"11193"},{"id":"6546","relation":"dissertation_contains","status":"public"}]},"doi":"10.1534/g3.117.300452","publication":"G3: Genes, Genomes, Genetics","issue":"3","acknowledged_ssus":[{"_id":"LifeSc"}],"oa":1,"date_updated":"2024-03-25T23:30:15Z","acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","month":"03","intvolume":"         8","date_published":"2018-03-01T00:00:00Z","year":"2018","page":"845 - 857","external_id":{"isi":["000426693300011"]}},{"language":[{"iso":"eng"}],"pubrep_id":"1066","year":"2018","page":"27","date_updated":"2025-06-02T08:53:45Z","file":[{"relation":"main_file","access_level":"open_access","checksum":"ba3adafd36fe200385ccda583063b9eb","creator":"system","file_size":4202966,"content_type":"application/pdf","file_id":"5493","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T11:53:32Z","file_name":"IST-2018-1066-v1+1_techreport.pdf"},{"checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","access_level":"closed","relation":"main_file","content_type":"text/plain","file_id":"6402","file_size":322,"creator":"dernst","date_updated":"2020-07-14T12:47:00Z","date_created":"2019-05-10T13:22:12Z","file_name":"authors-names.txt"}],"title":"Cost analysis of nondeterministic probabilistic programs","author":[{"last_name":"Anonymous","first_name":"1","full_name":"Anonymous, 1"},{"full_name":"Anonymous, 2","first_name":"2","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"},{"first_name":"5","last_name":"Anonymous","full_name":"Anonymous, 5"},{"last_name":"Anonymous","first_name":"6","full_name":"Anonymous, 6"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","month":"11","alternative_title":["IST Austria Technical Report"],"date_published":"2018-11-11T00:00:00Z","publisher":"IST Austria","related_material":{"record":[{"relation":"later_version","status":"public","id":"6175"}]},"oa_version":"Published Version","publication_status":"published","ddc":["000"],"_id":"5457","date_created":"2018-12-12T11:39:26Z","status":"public","day":"11","publication_identifier":{"issn":["2664-1690"]},"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.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","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.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria; 2018.","mla":"Anonymous, 1, et al. <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","type":"technical_report","scopus_import":1,"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."}]},{"publication_status":"published","quality_controlled":"1","_id":"546","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","citation":{"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>","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>.","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>","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","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.","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>."},"language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"publist_id":"7268","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Neural stem cells in neuropsychiatric disorders","author":[{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"publisher":"Elsevier","oa_version":"None","isi":1,"publication":"Current Opinion in Neurobiology","doi":"10.1016/j.conb.2017.12.005","day":"01","status":"public","date_created":"2018-12-11T11:47:06Z","volume":48,"year":"2018","external_id":{"isi":["000427101600018"]},"page":"131 - 138","issue":"2","date_updated":"2023-09-13T09:01:56Z","date_published":"2018-02-01T00:00:00Z","intvolume":"        48","month":"02"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"extern":"1","citation":{"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>","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>.","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>","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.","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.","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.","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>."},"volume":21,"day":"06","status":"public","date_created":"2018-12-11T11:47:06Z","_id":"547","doi":"10.1038/s41593-017-0053-5","publication_status":"published","publication":"Nature Neuroscience","isi":1,"oa_version":"None","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.","publisher":"Nature Publishing Group","month":"06","intvolume":"        21","date_published":"2018-06-06T00:00:00Z","issue":"2","title":"Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans","author":[{"full_name":"Gstrein, Thomas","last_name":"Gstrein","first_name":"Thomas"},{"first_name":"Andrew","last_name":"Edwards","full_name":"Edwards, Andrew"},{"last_name":"Přistoupilová","first_name":"Anna","full_name":"Přistoupilová, Anna"},{"full_name":"Leca, Ines","first_name":"Ines","last_name":"Leca"},{"full_name":"Breuss, Martin","last_name":"Breuss","first_name":"Martin"},{"first_name":"Sandra","last_name":"Pilat Carotta","full_name":"Pilat Carotta, Sandra"},{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tripathy, Ratna","first_name":"Ratna","last_name":"Tripathy"},{"first_name":"Anna","last_name":"Traunbauer","full_name":"Traunbauer, Anna"},{"full_name":"Hochstoeger, Tobias","last_name":"Hochstoeger","first_name":"Tobias"},{"full_name":"Rosoklija, Gavril","last_name":"Rosoklija","first_name":"Gavril"},{"last_name":"Repic","first_name":"Marco","full_name":"Repic, Marco"},{"first_name":"Lukas","last_name":"Landler","full_name":"Landler, Lukas"},{"full_name":"Stránecký, Viktor","last_name":"Stránecký","first_name":"Viktor"},{"last_name":"Dürnberger","first_name":"Gerhard","full_name":"Dürnberger, Gerhard"},{"full_name":"Keane, Thomas","first_name":"Thomas","last_name":"Keane"},{"first_name":"Johannes","last_name":"Zuber","full_name":"Zuber, Johannes"},{"full_name":"Adams, David","first_name":"David","last_name":"Adams"},{"last_name":"Flint","first_name":"Jonathan","full_name":"Flint, Jonathan"},{"last_name":"Honzik","first_name":"Tomas","full_name":"Honzik, Tomas"},{"last_name":"Gut","first_name":"Marta","full_name":"Gut, Marta"},{"first_name":"Sergi","last_name":"Beltran","full_name":"Beltran, Sergi"},{"last_name":"Mechtler","first_name":"Karl","full_name":"Mechtler, Karl"},{"full_name":"Sherr, Elliott","last_name":"Sherr","first_name":"Elliott"},{"full_name":"Kmoch, Stanislav","first_name":"Stanislav","last_name":"Kmoch"},{"last_name":"Gut","first_name":"Ivo","full_name":"Gut, Ivo"},{"first_name":"David","last_name":"Keays","full_name":"Keays, David"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T08:59:52Z","publist_id":"7267","external_id":{"isi":["000424269900012"]},"page":"207 - 217","article_processing_charge":"No","year":"2018","language":[{"iso":"eng"}]},{"quality_controlled":"1","_id":"55","scopus_import":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","citation":{"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>.","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>","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>.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","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.","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>"},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9547-2494","last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","full_name":"Metzler, Sina"},{"first_name":"Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"title":"Protection against the lethal side effects of social immunity in ants","publisher":"Cell Press","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"publist_id":"7999","article_processing_charge":"No","day":"08","status":"public","date_created":"2018-12-11T11:44:23Z","volume":28,"oa_version":"Published Version","isi":1,"publication":"Current Biology","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"doi":"10.1016/j.cub.2018.08.063","oa":1,"issue":"19","date_updated":"2023-09-15T12:06:46Z","date_published":"2018-10-08T00:00:00Z","intvolume":"        28","month":"10","year":"2018","page":"R1139 - R1140","external_id":{"isi":["000446693400008"]}},{"citation":{"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>","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.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","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.","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>.","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>","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>."},"publication_identifier":{"issn":["00103616"]},"type":"journal_article","arxiv":1,"scopus_import":1,"abstract":[{"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.).","lang":"eng"}],"_id":"554","quality_controlled":"1","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27"}],"publication_status":"published","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","last_name":"Reuvers","full_name":"Reuvers, Robin"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"title":"The Bogoliubov free energy functional II: The dilute Limit","publist_id":"7260","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"volume":360,"date_created":"2018-12-11T11:47:09Z","day":"01","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"doi":"10.1007/s00220-017-3064-x","publication":"Communications in Mathematical Physics","oa_version":"Submitted Version","intvolume":"       360","month":"05","date_published":"2018-05-01T00:00:00Z","date_updated":"2021-01-12T08:02:35Z","issue":"1","oa":1,"page":"347-403","external_id":{"arxiv":["1511.05953"]},"year":"2018"},{"oa_version":"Submitted Version","isi":1,"publication":"Current Opinion in Structural Biology","doi":"10.1016/j.sbi.2017.12.002","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/125524/"}],"day":"01","status":"public","date_created":"2018-12-11T11:47:09Z","volume":50,"year":"2018","page":"65 - 74","external_id":{"isi":["000443661300011"]},"oa":1,"date_updated":"2023-09-11T14:07:03Z","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_published":"2018-06-01T00:00:00Z","month":"06","intvolume":"        50","publication_status":"published","quality_controlled":"1","_id":"555","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"}],"scopus_import":"1","type":"journal_article","citation":{"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>","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>.","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.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","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.","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>."},"article_type":"original","language":[{"iso":"eng"}],"publist_id":"7259","department":[{"_id":"MaLo"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","author":[{"full_name":"Richter, Ralf","last_name":"Richter","first_name":"Ralf"},{"full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"full_name":"Day, Anthony","first_name":"Anthony","last_name":"Day"},{"full_name":"Kwok, Jessica","last_name":"Kwok","first_name":"Jessica"}],"publisher":"Elsevier"},{"doi":"10.1007/s00023-018-0723-1","publication":"Annales Henri Poincare","ec_funded":1,"oa_version":"Published Version","volume":19,"status":"public","day":"13","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:09Z","ddc":["500"],"external_id":{"arxiv":["1704.05809"]},"page":"3663-3742","year":"2018","intvolume":"        19","month":"11","date_published":"2018-11-13T00:00:00Z","issue":"12","oa":1,"date_updated":"2024-02-20T10:48:17Z","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"},{"grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:03Z","arxiv":1,"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["1424-0637"]},"citation":{"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>.","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.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","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.","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>","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>.","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>"},"quality_controlled":"1","_id":"556","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publist_id":"7258","article_processing_charge":"Yes (via OA deal)","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:03Z","date_created":"2019-01-21T15:18:55Z","file_name":"2018_Annales_Betea.pdf","relation":"main_file","checksum":"0c38abe73569b7166b7487ad5d23cc68","access_level":"open_access","file_size":3084674,"creator":"dernst","content_type":"application/pdf","file_id":"5866"}],"author":[{"first_name":"Dan","last_name":"Betea","full_name":"Betea, Dan"},{"full_name":"Bouttier, Jeremie","last_name":"Bouttier","first_name":"Jeremie"},{"last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter"},{"first_name":"Mirjana","last_name":"Vuletic","full_name":"Vuletic, Mirjana"}],"title":"The free boundary Schur process and applications I","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","day":"07","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_created":"2018-12-12T12:31:35Z","_id":"5569","ddc":["579"],"file_date_updated":"2020-07-14T12:47:04Z","type":"research_data","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"citation":{"ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>","short":"T. Bergmiller, N. Nikolic, (2018).","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>.","apa":"Bergmiller, T., &#38; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>","mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>."},"oa_version":"Published Version","related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"doi":"10.15479/AT:ISTA:74","file":[{"date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","relation":"main_file","checksum":"61ebb92213cfffeba3ddbaff984b81af","access_level":"open_access","creator":"system","file_size":3558703796,"file_id":"5637","content_type":"application/zip"},{"file_size":1830422606,"creator":"system","file_id":"5638","content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"bf26649af310ef6892d68576515cde6d","file_name":"IST-2018-74-v1+3_15-07-31.zip","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:55Z"},{"file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z","date_updated":"2020-07-14T12:47:04Z","file_id":"5639","content_type":"application/zip","file_size":2140849248,"creator":"system","relation":"main_file","access_level":"open_access","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd"}],"author":[{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Time-lapse microscopy data","date_updated":"2024-02-21T13:44:45Z","keyword":["microscopy","microfluidics"],"publisher":"Institute of Science and Technology Austria","month":"02","has_accepted_license":"1","datarep_id":"74","date_published":"2018-02-07T00:00:00Z","year":"2018","publist_id":"7385","license":"https://creativecommons.org/publicdomain/zero/1.0/","department":[{"_id":"CaGu"}],"article_processing_charge":"No"},{"doi":"10.15479/AT:ISTA:82","oa_version":"Published Version","related_material":{"link":[{"relation":"research_paper","url":"https://doi.org/10.1007/978-3-319-24947-6_23"}]},"contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","contributor_type":"researcher"}],"file_date_updated":"2020-07-14T12:47:05Z","type":"research_data","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"citation":{"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>","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>.","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>","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","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>.","ieee":"H. 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Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","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>."},"day":"04","status":"public","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["001"],"_id":"5573","date_created":"2018-12-12T12:31:36Z","department":[{"_id":"VlKo"}],"article_processing_charge":"No","year":"2018","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"01","date_published":"2018-01-04T00:00:00Z","datarep_id":"82","file":[{"checksum":"53c17082848e12f3c2e1b4185b578208","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5600","file_size":1737958,"creator":"system","date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:02:34Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip"}],"oa":1,"title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","author":[{"full_name":"Alhaija, Hassan","last_name":"Alhaija","first_name":"Hassan"},{"full_name":"Sellent, Anita","last_name":"Sellent","first_name":"Anita"},{"first_name":"Daniel","last_name":"Kondermann","full_name":"Kondermann, Daniel"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:41:17Z","keyword":["graph matching","quadratic assignment problem<"]},{"department":[{"_id":"E-Lib"}],"article_processing_charge":"No","year":"2018","publisher":"Institute of Science and Technology Austria","month":"01","has_accepted_license":"1","date_published":"2018-01-16T00:00:00Z","datarep_id":"86","file":[{"date_created":"2018-12-12T13:05:14Z","date_updated":"2020-07-14T12:47:05Z","file_name":"IST-2018-86-v1+1_Data_Check_IOP_Scopus_vs._Publisher.zip","relation":"main_file","access_level":"open_access","checksum":"c7a61147bd15cb4ae45878d270628c06","content_type":"application/zip","file_id":"5642","file_size":12283857,"creator":"system"}],"title":"Data Check IOP Scopus vs. Publisher","oa":1,"author":[{"full_name":"Villányi, Márton","last_name":"Villányi","orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:42:21Z","keyword":["Publication analysis","Bibliography","Open Access"],"doi":"10.15479/AT:ISTA:86","oa_version":"Submitted Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"278"}]},"file_date_updated":"2020-07-14T12:47:05Z","type":"research_data","abstract":[{"lang":"ger","text":"Comparison of Scopus' and publisher's data on Austrian publication output at IOP. "}],"citation":{"apa":"Villányi, M. (2018). Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:86\">https://doi.org/10.15479/AT:ISTA:86</a>","mla":"Villányi, Márton. <i>Data Check IOP Scopus vs. Publisher</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>.","ama":"Villányi M. Data Check IOP Scopus vs. Publisher. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>","short":"M. Villányi, (2018).","ieee":"M. Villányi, “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018.","ista":"Villányi M. 2018. 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Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:87\">10.15479/AT:ISTA:87</a>.","apa":"Villányi, M. (2018). Data Check RSC Scopus vs. FWF. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:87\">https://doi.org/10.15479/AT:ISTA:87</a>","chicago":"Villányi, Márton. “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:87\">https://doi.org/10.15479/AT:ISTA:87</a>.","ista":"Villányi M. 2018. Data Check RSC Scopus vs. FWF, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:87\">10.15479/AT:ISTA:87</a>.","short":"M. Villányi, (2018).","ieee":"M. Villányi, “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018.","ama":"Villányi M. 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