[{"title":"Boosting expensive synchronizing heuristics","quality_controlled":"1","citation":{"mla":"Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>, vol. 167, no. 4, 114203, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>.","apa":"Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., &#38; Yenigün, H. (2021). Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>","chicago":"Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>.","ama":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. 2021;167(4). doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>","short":"N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021).","ista":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203.","ieee":"N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” <i>Expert Systems with Applications</i>, vol. 167, no. 4. Elsevier, 2021."},"date_created":"2020-12-02T13:34:25Z","oa":1,"article_number":"114203","article_processing_charge":"No","file_date_updated":"2020-12-02T13:33:51Z","doi":"10.1016/j.eswa.2020.114203","date_published":"2021-04-01T00:00:00Z","intvolume":"       167","has_accepted_license":"1","publication":"Expert Systems with Applications","day":"01","acknowledgement":"This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11.","volume":167,"article_type":"original","department":[{"_id":"ToHe"}],"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"year":"2021","month":"04","publication_identifier":{"issn":["09574174"]},"isi":1,"publication_status":"published","external_id":{"isi":["000640531100038"]},"_id":"8912","issue":"4","type":"journal_article","ddc":["000"],"oa_version":"Submitted Version","file":[{"creator":"esarac","file_id":"8913","relation":"main_file","file_name":"synchroPaperRevised.pdf","file_size":634967,"checksum":"600c2f81bc898a725bcfa7cf26ff4fed","date_created":"2020-12-02T13:33:51Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-12-02T13:33:51Z"}],"publisher":"Elsevier","status":"public","author":[{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"},{"first_name":"Ömer Faruk","full_name":"Altun, Ömer Faruk","last_name":"Altun"},{"full_name":"Atam, Kamil Tolga","last_name":"Atam","first_name":"Kamil Tolga"},{"first_name":"Sertac","full_name":"Karahoda, Sertac","last_name":"Karahoda"},{"last_name":"Kaya","full_name":"Kaya, Kamer","first_name":"Kamer"},{"last_name":"Yenigün","full_name":"Yenigün, Hüsnü","first_name":"Hüsnü"}],"scopus_import":"1","abstract":[{"text":"For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T11:19:00Z"},{"isi":1,"publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"month":"02","year":"2021","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"department":[{"_id":"NiBa"}],"article_type":"original","publisher":"Wiley","type":"journal_article","oa_version":"Published Version","issue":"2","_id":"8928","external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"publication_status":"published","author":[{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"status":"public","date_updated":"2023-08-04T11:19:26Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13065"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"scopus_import":"1","page":"270-283","title":"Genomic inference of complex domestication histories in three Solanaceae species","oa":1,"citation":{"short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>."},"date_created":"2020-12-06T23:01:16Z","quality_controlled":"1","doi":"10.1111/jeb.13723","article_processing_charge":"No","volume":34,"publication":"Journal of Evolutionary Biology","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","day":"01","pmid":1,"intvolume":"        34","date_published":"2021-02-01T00:00:00Z"},{"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","article_number":"110750","oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>."},"date_created":"2020-12-09T14:48:28Z","quality_controlled":"1","doi":"10.1016/j.plantsci.2020.110750","file_date_updated":"2021-02-04T07:49:25Z","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":303,"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","day":"01","publication":"Plant Science","pmid":1,"has_accepted_license":"1","intvolume":"       303","date_published":"2021-02-01T00:00:00Z","isi":1,"publication_identifier":{"issn":["0168-9452"]},"month":"02","year":"2021","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"department":[{"_id":"JiFr"},{"_id":"Bio"}],"article_type":"original","publisher":"Elsevier","file":[{"file_name":"2021_PlantScience_Gelova.pdf","relation":"main_file","creator":"dernst","file_id":"9083","date_updated":"2021-02-04T07:49:25Z","content_type":"application/pdf","access_level":"open_access","date_created":"2021-02-04T07:49:25Z","file_size":12563728,"success":1,"checksum":"a7f2562bdca62d67dfa88e271b62a629"}],"oa_version":"Published Version","ddc":["580"],"type":"journal_article","_id":"8931","external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"publication_status":"published","author":[{"orcid":"0000-0003-4783-1752","last_name":"Gelová","full_name":"Gelová, Zuzana","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"last_name":"Brunoud","full_name":"Brunoud, Géraldine","first_name":"Géraldine"},{"orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","last_name":"Li","full_name":"Li, Lanxin"},{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"status":"public","date_updated":"2024-10-29T10:22:43Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"scopus_import":"1"},{"file_date_updated":"2021-12-23T23:30:04Z","doi":"10.15479/AT:ISTA:8934","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"article_processing_charge":"No","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","day":"01","date_published":"2021-01-01T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","page":"278","title":"Parameterized and algebro-geometric advances in static program analysis","oa":1,"date_created":"2020-12-10T12:17:07Z","citation":{"ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","status":"public","author":[{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2025-06-02T08:53:47Z","related_material":{"record":[{"id":"1386","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1437"},{"id":"639","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6918"},{"id":"6490","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7158"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"relation":"part_of_dissertation","status":"public","id":"949"},{"id":"311","status":"public","relation":"part_of_dissertation"},{"id":"7810","status":"public","relation":"part_of_dissertation"},{"id":"8089","relation":"part_of_dissertation","status":"public"},{"id":"8728","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6175"},{"id":"6340","relation":"part_of_dissertation","status":"public"},{"id":"6378","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6380"},{"status":"public","relation":"part_of_dissertation","id":"66"},{"id":"6780","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7014"}]},"abstract":[{"lang":"eng","text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades."}],"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"year":"2021","month":"01","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"8934","file":[{"file_name":"Thesis-pdfa.pdf","creator":"akafshda","file_id":"8969","relation":"main_file","content_type":"application/pdf","embargo":"2021-12-22","access_level":"open_access","date_updated":"2021-12-23T23:30:04Z","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_size":5251507,"date_created":"2020-12-22T20:08:44Z"},{"checksum":"1661df7b393e6866d2460eba3c905130","file_size":10636756,"embargo_to":"open_access","date_created":"2020-12-22T20:08:50Z","access_level":"closed","content_type":"application/zip","date_updated":"2021-03-04T23:30:04Z","file_id":"8970","creator":"akafshda","relation":"source_file","file_name":"source.zip"}],"type":"dissertation","ddc":["005"],"oa_version":"Published Version"},{"has_accepted_license":"1","intvolume":"        66","date_published":"2021-07-01T00:00:00Z","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","day":"01","publication":"Discrete & Computational Geometry","volume":66,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"doi":"10.1007/s00454-020-00250-8","file_date_updated":"2021-08-06T09:52:29Z","citation":{"ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. 2021;66(1):386-434. doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete &#38; Computational Geometry. 66(1), 386–434.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>.","apa":"Boissonnat, J.-D., Kachanovich, S., &#38; Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>."},"date_created":"2020-12-12T11:07:02Z","quality_controlled":"1","oa":1,"title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","page":"386-434","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"abstract":[{"lang":"eng","text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric."}],"date_updated":"2023-09-05T15:02:40Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Siargey","full_name":"Kachanovich, Siargey","last_name":"Kachanovich"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"ddc":["516"],"file":[{"creator":"kschuh","file_id":"9795","relation":"main_file","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","success":1,"checksum":"c848986091e56699dc12de85adb1e39c","file_size":983307,"date_created":"2021-08-06T09:52:29Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-08-06T09:52:29Z"}],"oa_version":"Published Version","type":"journal_article","external_id":{"isi":["000597770300001"]},"publication_status":"published","_id":"8940","issue":"1","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"article_type":"original","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"year":"2021","month":"07"},{"file_date_updated":"2021-08-11T10:28:06Z","doi":"10.1016/j.ydbio.2020.12.014","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"publication":"Developmental Biology","day":"01","acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","volume":474,"date_published":"2021-06-01T00:00:00Z","intvolume":"       474","has_accepted_license":"1","page":"71-81","title":"Reassembling gastrulation","oa":1,"quality_controlled":"1","date_created":"2020-12-22T09:53:34Z","citation":{"mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>"},"status":"public","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-07T13:30:01Z","scopus_import":"1","keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"related_material":{"record":[{"id":"12891","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.","lang":"eng"}],"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"month":"06","year":"2021","publication_identifier":{"issn":["0012-1606"]},"isi":1,"article_type":"original","department":[{"_id":"CaHe"}],"publisher":"Elsevier","external_id":{"isi":["000639461800008"]},"publication_status":"published","_id":"8966","file":[{"file_id":"9880","creator":"kschuh","relation":"main_file","file_name":"2021_DevBiology_Schauer.pdf","checksum":"fa2a5731fd16ab171b029f32f031c440","success":1,"file_size":1440321,"date_created":"2021-08-11T10:28:06Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-08-11T10:28:06Z"}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2010054118"}],"abstract":[{"lang":"eng","text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching."}],"scopus_import":"1","date_updated":"2023-08-04T11:20:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"last_name":"Düllberg","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","last_name":"Auer","orcid":"0000-0002-3580-2906"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926"},{"first_name":"Katrin","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2429-7668","last_name":"Loibl","full_name":"Loibl, Katrin"},{"full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["33443153"],"isi":["000607270100018"]},"publication_status":"published","issue":"1","_id":"8988","publisher":"National Academy of Sciences","department":[{"_id":"MaLo"},{"_id":"MiSi"}],"article_type":"original","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"isi":1,"project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016"}],"month":"01","year":"2021","intvolume":"       118","date_published":"2021-01-05T00:00:00Z","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","publication":"PNAS","day":"05","volume":118,"pmid":1,"article_processing_charge":"No","doi":"10.1073/pnas.2010054118","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"citation":{"chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>PNAS</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. PNAS. 118(1), e2010054118.","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, PNAS 118 (2021).","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>"},"date_created":"2021-01-03T23:01:23Z","quality_controlled":"1","oa":1,"article_number":"e2010054118","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1"},{"page":"151-165","title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","oa":1,"citation":{"ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. 2021;14(1):151-165. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>","ieee":"S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” <i>Molecular Plant</i>, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.","ista":"Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.","mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>.","apa":"Tan, S., Luschnig, C., &#38; Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>","chicago":"Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>."},"date_created":"2021-01-03T23:01:23Z","quality_controlled":"1","doi":"10.1016/j.molp.2020.11.004","file_date_updated":"2021-01-07T14:03:53Z","article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":14,"acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","day":"04","publication":"Molecular Plant","pmid":1,"intvolume":"        14","has_accepted_license":"1","date_published":"2021-01-04T00:00:00Z","isi":1,"publication_identifier":{"issn":["16742052"],"eissn":["17529867"]},"year":"2021","month":"01","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"723-2015","name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"JiFr"}],"article_type":"original","publisher":"Elsevier","oa_version":"Published Version","file":[{"date_updated":"2021-01-07T14:03:53Z","access_level":"open_access","content_type":"application/pdf","date_created":"2021-01-07T14:03:53Z","file_size":871088,"checksum":"917e60e57092f22e16beac70b1775ea6","success":1,"file_name":"2020_MolecularPlant_Tan.pdf","relation":"main_file","file_id":"8995","creator":"dernst"}],"ddc":["580"],"type":"journal_article","issue":"1","_id":"8992","publication_status":"published","external_id":{"isi":["000605359400014"],"pmid":["33186755"]},"author":[{"orcid":"0000-0002-0471-8285","last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_updated":"2023-08-04T11:21:13Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network."}],"scopus_import":"1"},{"article_type":"original","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"year":"2021","month":"01","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"isi":1,"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"_id":"8993","issue":"1","external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"publication_status":"published","type":"journal_article","oa_version":"Published Version","publisher":"National Academy of Sciences","author":[{"first_name":"Lindy","full_name":"Abas, Lindy","last_name":"Abas"},{"last_name":"Kolb","full_name":"Kolb, Martina","first_name":"Martina"},{"first_name":"Johannes","last_name":"Stadlmann","full_name":"Stadlmann, Johannes"},{"last_name":"Janacek","full_name":"Janacek, Dorina P.","first_name":"Dorina P."},{"first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1581-881X","full_name":"Lukic, Kristina","last_name":"Lukic"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"full_name":"Mach, Lukas","last_name":"Mach","first_name":"Lukas"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Ulrich Z.","last_name":"Hammes","full_name":"Hammes, Ulrich Z."}],"status":"public","scopus_import":"1","abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2020857118"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-07T13:29:23Z","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","quality_controlled":"1","date_created":"2021-01-03T23:01:23Z","citation":{"mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>.","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>PNAS</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>PNAS</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>PNAS</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>"},"article_number":"e2020857118","oa":1,"ec_funded":1,"article_processing_charge":"No","doi":"10.1073/pnas.2020857118","date_published":"2021-01-05T00:00:00Z","intvolume":"       118","pmid":1,"volume":118,"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","day":"05","publication":"PNAS"},{"quality_controlled":"1","citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>."},"date_created":"2021-01-08T07:16:18Z","article_number":"e1008529","oa":1,"title":"Minimal biophysical model of combined antibiotic action","date_published":"2021-01-07T00:00:00Z","has_accepted_license":"1","intvolume":"        17","volume":17,"acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","day":"07","publication":"PLOS Computational Biology","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-02-04T12:30:48Z","doi":"10.1371/journal.pcbi.1008529","_id":"8997","publication_status":"published","external_id":{"isi":["000608045000010"]},"oa_version":"Published Version","type":"journal_article","file":[{"relation":"main_file","creator":"dernst","file_id":"9092","file_name":"2021_PlosComBio_Kavcic.pdf","date_created":"2021-02-04T12:30:48Z","success":1,"checksum":"e29f2b42651bef8e034781de8781ffac","file_size":3690053,"date_updated":"2021-02-04T12:30:48Z","content_type":"application/pdf","access_level":"open_access"}],"ddc":["570"],"publisher":"Public Library of Science","article_type":"original","department":[{"_id":"GaTk"}],"month":"01","year":"2021","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication_identifier":{"issn":["1553-7358"]},"abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7673"},{"id":"8930","relation":"research_data","status":"public"}]},"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-02-21T12:41:41Z","author":[{"last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"status":"public"},{"article_number":"58","oa":1,"citation":{"short":"K. Avila, B. Hof, Entropy 23 (2021).","ieee":"K. Avila and B. Hof, “Second-order phase transition in counter-rotating taylor-couette flow experiment,” <i>Entropy</i>, vol. 23, no. 1. MDPI, 2021.","ista":"Avila K, Hof B. 2021. Second-order phase transition in counter-rotating taylor-couette flow experiment. Entropy. 23(1), 58.","ama":"Avila K, Hof B. Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. 2021;23(1). doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>","mla":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>, vol. 23, no. 1, 58, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/e23010058\">10.3390/e23010058</a>.","chicago":"Avila, Kerstin, and Björn Hof. “Second-Order Phase Transition in Counter-Rotating Taylor-Couette Flow Experiment.” <i>Entropy</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>.","apa":"Avila, K., &#38; Hof, B. (2021). Second-order phase transition in counter-rotating taylor-couette flow experiment. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e23010058\">https://doi.org/10.3390/e23010058</a>"},"date_created":"2021-01-10T23:01:17Z","quality_controlled":"1","title":"Second-order phase transition in counter-rotating taylor-couette flow experiment","volume":23,"publication":"Entropy","day":"01","acknowledgement":"This research was funded by the Central Research Development Fund of the University of\r\nBremen grant number ZF04B /2019/FB04 Avila_Kerstin (“Independent Project for Postdocs”). Shreyas Jalikop is acknowledged for recording some of the lifetime measurements\r\n","pmid":1,"has_accepted_license":"1","intvolume":"        23","date_published":"2021-01-01T00:00:00Z","doi":"10.3390/e23010058","file_date_updated":"2021-01-11T07:50:32Z","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"MDPI","ddc":["530"],"oa_version":"Published Version","file":[{"file_id":"9003","creator":"dernst","relation":"main_file","file_name":"2021_Entropy_Avila.pdf","success":1,"file_size":9456389,"checksum":"3ba3dd8b7eecff713b72c5e9ba30d626","date_created":"2021-01-11T07:50:32Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-01-11T07:50:32Z"}],"type":"journal_article","_id":"8999","issue":"1","external_id":{"pmid":["33396499"],"isi":["000610135400001"]},"publication_status":"published","isi":1,"publication_identifier":{"eissn":["1099-4300"]},"year":"2021","month":"01","department":[{"_id":"BjHo"}],"article_type":"original","date_updated":"2023-08-07T13:31:07Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not\r\narise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. "}],"scopus_import":"1","author":[{"full_name":"Avila, Kerstin","last_name":"Avila","id":"fcf74381-53e1-11eb-a6dc-b0e2acf78757","first_name":"Kerstin"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"author":[{"last_name":"Rychlewicz","full_name":"Rychlewicz, Kamil P","first_name":"Kamil P","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"status":"public","abstract":[{"text":"The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10435"}],"scopus_import":"1","date_updated":"2023-08-04T10:43:39Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["0024-6093"],"eissn":["1469-2120"]},"year":"2021","month":"04","oa_version":"Preprint","type":"journal_article","issue":"2","_id":"6965","publication_status":"published","external_id":{"isi":["000594805800001"],"arxiv":["1910.10435"]},"publisher":"Wiley","article_processing_charge":"No","doi":"10.1112/blms.12442","intvolume":"        53","date_published":"2021-04-01T00:00:00Z","volume":53,"day":"01","publication":"Bulletin of the London Mathematical Society","title":"The positivity of local equivariant Hirzebruch class for toric varieties","page":"560-574","citation":{"chicago":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2021. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>.","apa":"Rychlewicz, K. P. (2021). The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12442\">https://doi.org/10.1112/blms.12442</a>","mla":"Rychlewicz, Kamil P. “The Positivity of Local Equivariant Hirzebruch Class for Toric Varieties.” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2, Wiley, 2021, pp. 560–74, doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>.","ista":"Rychlewicz KP. 2021. The positivity of local equivariant Hirzebruch class for toric varieties. Bulletin of the London Mathematical Society. 53(2), 560–574.","ieee":"K. P. Rychlewicz, “The positivity of local equivariant Hirzebruch class for toric varieties,” <i>Bulletin of the London Mathematical Society</i>, vol. 53, no. 2. Wiley, pp. 560–574, 2021.","short":"K.P. Rychlewicz, Bulletin of the London Mathematical Society 53 (2021) 560–574.","ama":"Rychlewicz KP. The positivity of local equivariant Hirzebruch class for toric varieties. <i>Bulletin of the London Mathematical Society</i>. 2021;53(2):560-574. doi:<a href=\"https://doi.org/10.1112/blms.12442\">10.1112/blms.12442</a>"},"date_created":"2019-10-24T08:04:09Z","arxiv":1,"quality_controlled":"1","oa":1},{"intvolume":"        24","date_published":"2021-08-23T00:00:00Z","volume":24,"day":"23","acknowledgement":"We thank S. Butler, T. Carmichael and members of the laboratory of B.G.N. for helpful discussions and comments on the manuscript; N. Vishlaghi and F. Turcios-Hernandez for technical assistance, and J. Lee, S.-K. Lee, H. Shinagawa and K. Yoshikawa for valuable reagents. We also thank the UCLA Eli and Edythe Broad Stem Cell Research Center (BSCRC) and Intellectual and Developmental Disabilities Research Center microscopy cores for access to imaging facilities. This work was supported by grants from the California Institute for Regenerative Medicine (CIRM) (DISC1-08819 to B.G.N.), the National Institute of Health (R01NS089817, R01DA051897 and P50HD103557 to B.G.N.; K08NS119747 to R.A.S.; K99HD096105 to M.W.; R01MH123922, R01MH121521 and P50HD103557 to M.J.G.; R01GM099134 to K.P.; R01NS103788 to W.E.L.; R01NS088571 to J.M.P.; R01NS030549 and R01AG050474 to I.M.), and research awards from the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program (to B.G.N.), the BSCRC Innovation Program (to B.G.N., K.P. and W.E.L.), the UCLA BSCRC Steffy Brain Aging Research Fund (to B.G.N. and W.E.L.) and the UCLA Clinical and Translational Science Institute (to B.G.N.), Paul Allen Family Foundation Frontiers Group (to K.P. and W.E.L.), the March of Dimes Foundation (to W.E.L.) and the Simons Foundation Autism Research Initiative Bridge to Independence Program (to R.A.S. and M.J.G.). R.A.S. was also supported by the UCLA/NINDS Translational Neuroscience Training Grant (R25NS065723), a Research and Training Fellowship from the American Epilepsy Society, a Taking Flight Award from CURE Epilepsy and a Clinician Scientist training award from the UCLA BSCRC. J.E.B. was supported by the UCLA BSCRC Rose Hills Foundation Graduate Scholarship Training Program. M.W. was supported by postdoctoral training awards provided by the UCLA BSCRC and the Uehara Memorial Foundation. O.A.M. and A.K. were supported in part by the UCLA-California State University Northridge CIRM-Bridges training program (EDUC2-08411). We also acknowledge the support of the IDDRC Cells, Circuits and Systems Analysis, Microscopy and Genetics and Genomics Cores of the Semel Institute of Neuroscience at UCLA, which are supported by the NICHD (U54HD087101 and P50HD10355701). We lastly acknowledge support from a Quantitative and Computational Biosciences Collaboratory Postdoctoral Fellowship to S.M. and the Quantitative and Computational Biosciences Collaboratory community, directed by M. Pellegrini.","pmid":1,"article_processing_charge":"Yes","doi":"10.1038/s41593-021-00906-5","citation":{"ieee":"R. A. Samarasinghe <i>et al.</i>, <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i>, vol. 24. Springer Nature, 2021.","short":"R.A. Samarasinghe, O. Miranda, J.E. Buth, S. Mitchell, I. Ferando, M. Watanabe, A. Kurdian, P. Golshani, K. Plath, W.E. Lowry, J.M. Parent, I. Mody, B.G. Novitch, Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids, Springer Nature, 2021.","ista":"Samarasinghe RA, Miranda O, Buth JE, Mitchell S, Ferando I, Watanabe M, Kurdian A, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. 2021. Identification of neural oscillations and epileptiform changes in human brain organoids, Springer Nature, 32p.","ama":"Samarasinghe RA, Miranda O, Buth JE, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol 24. Springer Nature; 2021. doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>","chicago":"Samarasinghe, Ranmal A., Osvaldo Miranda, Jessie E. Buth, Simon Mitchell, Isabella Ferando, Momoko Watanabe, Arinnae Kurdian, et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>.","apa":"Samarasinghe, R. A., Miranda, O., Buth, J. E., Mitchell, S., Ferando, I., Watanabe, M., … Novitch, B. G. (2021). <i>Identification of neural oscillations and epileptiform changes in human brain organoids</i> (Vol. 24). Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00906-5\">https://doi.org/10.1038/s41593-021-00906-5</a>","mla":"Samarasinghe, Ranmal A., et al. <i>Identification of Neural Oscillations and Epileptiform Changes in Human Brain Organoids</i>. Vol. 24, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41593-021-00906-5\">10.1038/s41593-021-00906-5</a>."},"date_created":"2019-11-10T11:23:58Z","oa":1,"title":"Identification of neural oscillations and epileptiform changes in human brain organoids","page":"32","abstract":[{"lang":"eng","text":"Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-021-00906-5"}],"date_updated":"2023-08-04T10:49:44Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"author":[{"last_name":"Samarasinghe","full_name":"Samarasinghe, Ranmal A.","first_name":"Ranmal A."},{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","last_name":"Miranda","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889"},{"first_name":"Jessie E.","last_name":"Buth","full_name":"Buth, Jessie E."},{"first_name":"Simon","full_name":"Mitchell, Simon","last_name":"Mitchell"},{"first_name":"Isabella","full_name":"Ferando, Isabella","last_name":"Ferando"},{"first_name":"Momoko","full_name":"Watanabe, Momoko","last_name":"Watanabe"},{"last_name":"Kurdian","full_name":"Kurdian, Arinnae","first_name":"Arinnae"},{"last_name":"Golshani","full_name":"Golshani, Peyman","first_name":"Peyman"},{"last_name":"Plath","full_name":"Plath, Kathrin","first_name":"Kathrin"},{"first_name":"William E.","full_name":"Lowry, William E.","last_name":"Lowry"},{"last_name":"Parent","full_name":"Parent, Jack M.","first_name":"Jack M."},{"full_name":"Mody, Istvan","last_name":"Mody","first_name":"Istvan"},{"full_name":"Novitch, Bennett G.","last_name":"Novitch","first_name":"Bennett G."}],"status":"public","oa_version":"Published Version","type":"technical_report","_id":"6995","alternative_title":["Nature Neuroscience"],"publication_status":"published","external_id":{"pmid":["34426698 "],"isi":["000687516300001"]},"publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"isi":1,"publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"year":"2021","month":"08"},{"author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"first_name":"Hans J","full_name":"Herrmann, Hans J","last_name":"Herrmann"},{"full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis","first_name":"Lucilla"}],"status":"public","scopus_import":"1","abstract":[{"text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T10:46:29Z","article_type":"original","department":[{"_id":"GaTk"}],"month":"05","year":"2021","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"publication_identifier":{"eissn":["1872-8286"],"issn":["0925-2312"]},"_id":"7463","external_id":{"isi":["000704086300015"]},"publication_status":"published","oa_version":"Preprint","type":"journal_article","publisher":"Elsevier","ec_funded":1,"article_processing_charge":"No","doi":"10.1016/j.neucom.2020.05.126","date_published":"2021-05-13T00:00:00Z","intvolume":"       461","volume":461,"day":"13","acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","publication":"Neurocomputing","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","page":"657-666","quality_controlled":"1","date_created":"2020-02-06T16:09:14Z","citation":{"mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>","chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021."},"oa":1},{"abstract":[{"lang":"eng","text":"Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty."}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/remembering-novelty/"}]},"date_updated":"2023-08-04T10:47:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"author":[{"full_name":"Fredes Tolorza, Felipe A","last_name":"Fredes Tolorza","first_name":"Felipe A","id":"384825DA-F248-11E8-B48F-1D18A9856A87"},{"id":"371B3D6E-F248-11E8-B48F-1D18A9856A87","first_name":"Maria A","last_name":"Silva Sifuentes","full_name":"Silva Sifuentes, Maria A"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"first_name":"Kenta","last_name":"Kobayashi","full_name":"Kobayashi, Kenta"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"status":"public","ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-19T13:31:28Z","success":1,"checksum":"b7b9c8bc84a08befce365c675229a7d1","file_size":4915964,"date_created":"2020-10-19T13:31:28Z","file_name":"2021_CurrentBiology_Fredes.pdf","file_id":"8678","creator":"dernst","relation":"main_file"}],"_id":"7551","issue":"1","publication_status":"published","external_id":{"isi":["000614361000020"]},"publisher":"Elsevier","department":[{"_id":"MaJö"},{"_id":"RySh"}],"article_type":"original","isi":1,"month":"01","year":"2021","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"intvolume":"        31","has_accepted_license":"1","date_published":"2021-01-11T00:00:00Z","volume":31,"day":"11","publication":"Current Biology","acknowledgement":"We thank Peter Jonas and Peter Somogyi for critically reading the manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L. Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst, and Laura Burnett for technical assistance, as well as Robert Beattie for imaging assistance. This work was supported by a European Research Council Advanced Grant 694539 to R.S.","article_processing_charge":"No","ec_funded":1,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.cub.2020.09.074","file_date_updated":"2020-10-19T13:31:28Z","citation":{"apa":"Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi, K., Jösch, M. A., &#38; Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>","chicago":"Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner, Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>.","mla":"Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, p. P25–38.E5, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>.","ama":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. 2021;31(1):P25-38.E5. doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>","short":"F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.","ista":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. Current Biology. 31(1), P25–38.E5.","ieee":"F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, p. P25–38.E5, 2021."},"date_created":"2020-02-28T10:56:18Z","quality_controlled":"1","oa":1,"title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","page":"P25-38.E5"},{"citation":{"mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>.","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5."},"date_created":"2020-02-28T11:00:12Z","quality_controlled":"1","oa":1,"title":"Statistical analysis and optimality of neural systems","page":"1227-1241.e5","intvolume":"       109","date_published":"2021-04-07T00:00:00Z","volume":109,"publication":"Neuron","acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","day":"07","article_processing_charge":"No","ec_funded":1,"doi":"10.1016/j.neuron.2021.01.020","type":"journal_article","oa_version":"Preprint","_id":"7553","issue":"7","external_id":{"isi":["000637809600006"]},"publication_status":"published","publisher":"Cell Press","department":[{"_id":"GaTk"}],"isi":1,"month":"04","year":"2021","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"abstract":[{"lang":"eng","text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"15020"}]},"scopus_import":"1","date_updated":"2025-06-30T13:21:05Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"status":"public"},{"doi":"10.1142/S0129055X20600065","ec_funded":1,"article_processing_charge":"No","volume":33,"day":"01","publication":"Reviews in Mathematical Physics","date_published":"2021-01-01T00:00:00Z","intvolume":"        33","title":"The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime","article_number":"2060006","oa":1,"quality_controlled":"1","arxiv":1,"citation":{"ieee":"C. Boccato, “The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific, 2021.","short":"C. Boccato, Reviews in Mathematical Physics 33 (2021).","ista":"Boccato C. 2021. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. Reviews in Mathematical Physics. 33(1), 2060006.","ama":"Boccato C. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>","mla":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060006, World Scientific, 2021, doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>.","chicago":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>. World Scientific, 2021. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>.","apa":"Boccato, C. (2021). The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. World Scientific. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>"},"date_created":"2020-04-26T22:00:45Z","author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara","last_name":"Boccato","full_name":"Boccato, Chiara"}],"status":"public","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T10:50:13Z","scopus_import":"1","abstract":[{"text":"We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.00497"}],"month":"01","year":"2021","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"isi":1,"publication_identifier":{"issn":["0129-055X"]},"article_type":"original","department":[{"_id":"RoSe"}],"publisher":"World Scientific","_id":"7685","issue":"1","publication_status":"published","external_id":{"arxiv":["2001.00497"],"isi":["000613313200007"]},"type":"journal_article","oa_version":"Preprint"},{"oa_version":"None","type":"conference","citation":{"ama":"Träuble F, Dittadi A, Wuthrich M, et al. Representation learning for out-of-distribution generalization in reinforcement learning. In: <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>. ; 2021.","ieee":"F. Träuble <i>et al.</i>, “Representation learning for out-of-distribution generalization in reinforcement learning,” in <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, Virtual, 2021.","short":"F. Träuble, A. Dittadi, M. Wuthrich, F. Widmaier, P.V. Gehler, O. Winther, F. Locatello, O. Bachem, B. Schölkopf, S. Bauer, in:, ICML 2021 Workshop on Unsupervised Reinforcement Learning, 2021.","ista":"Träuble F, Dittadi A, Wuthrich M, Widmaier F, Gehler PV, Winther O, Locatello F, Bachem O, Schölkopf B, Bauer S. 2021. Representation learning for out-of-distribution generalization in reinforcement learning. ICML 2021 Workshop on Unsupervised Reinforcement Learning. ICML: International Conference on Machine Learning.","mla":"Träuble, Frederik, et al. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, 2021.","apa":"Träuble, F., Dittadi, A., Wuthrich, M., Widmaier, F., Gehler, P. V., Winther, O., … Bauer, S. (2021). Representation learning for out-of-distribution generalization in reinforcement learning. In <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>. Virtual.","chicago":"Träuble, Frederik, Andrea Dittadi, Manuel Wuthrich, Felix Widmaier, Peter Vincent Gehler, Ole Winther, Francesco Locatello, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” In <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, 2021."},"date_created":"2023-09-13T12:43:14Z","quality_controlled":"1","publication_status":"published","conference":{"start_date":"2021-07-23","name":"ICML: International Conference on Machine Learning","location":"Virtual","end_date":"2021-07-23"},"_id":"14332","department":[{"_id":"FrLo"}],"title":"Representation learning for out-of-distribution generalization in reinforcement learning","month":"07","year":"2021","abstract":[{"lang":"eng","text":"Learning data representations that are useful for various downstream tasks is a cornerstone of artificial intelligence. While existing methods are typically evaluated on downstream tasks such as classification or generative image quality, we propose to assess representations through their usefulness in downstream control tasks, such as reaching or pushing objects. By training over 10,000 reinforcement learning policies, we extensively evaluate to what extent different representation properties affect out-of-distribution (OOD) generalization. Finally, we demonstrate zero-shot transfer of these policies from simulation to the real world, without any domain randomization or fine-tuning. This paper aims to establish the first systematic characterization of the usefulness of learned representations for real-world OOD downstream tasks."}],"extern":"1","date_published":"2021-07-23T00:00:00Z","day":"23","publication":"ICML 2021 Workshop on Unsupervised Reinforcement Learning","date_updated":"2023-09-13T12:44:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","article_processing_charge":"No","author":[{"last_name":"Träuble","full_name":"Träuble, Frederik","first_name":"Frederik"},{"first_name":"Andrea","last_name":"Dittadi","full_name":"Dittadi, Andrea"},{"first_name":"Manuel","full_name":"Wuthrich, Manuel","last_name":"Wuthrich"},{"last_name":"Widmaier","full_name":"Widmaier, Felix","first_name":"Felix"},{"first_name":"Peter Vincent","last_name":"Gehler","full_name":"Gehler, Peter Vincent"},{"last_name":"Winther","full_name":"Winther, Ole","first_name":"Ole"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"}]},{"publisher":"Peking University","oa_version":"Submitted Version","type":"journal_article","_id":"14800","issue":"12","publication_status":"published","publication_identifier":{"issn":["1001-4861"]},"year":"2021","month":"10","department":[{"_id":"MaIb"}],"article_type":"review","date_updated":"2024-01-17T11:29:33Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. ","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.3866/PKU.WHXB202108017","open_access":"1"}],"scopus_import":"1","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang","orcid":"0000-0002-9515-4277"},{"first_name":"Wei","full_name":"Chen, Wei","last_name":"Chen"},{"first_name":"Ye","last_name":"Chen","full_name":"Chen, Ye"},{"full_name":"Chen, Yonghua","last_name":"Chen","first_name":"Yonghua"},{"last_name":"Chen","full_name":"Chen, Yu","first_name":"Yu"},{"first_name":"Feng","last_name":"Ding","full_name":"Ding, Feng"},{"last_name":"Fan","full_name":"Fan, Chunhai","first_name":"Chunhai"},{"first_name":"Hong Jin","last_name":"Fan","full_name":"Fan, Hong Jin"},{"first_name":"Zhanxi","last_name":"Fan","full_name":"Fan, Zhanxi"},{"last_name":"Gong","full_name":"Gong, Cheng","first_name":"Cheng"},{"first_name":"Yongji","last_name":"Gong","full_name":"Gong, Yongji"},{"first_name":"Qiyuan","full_name":"He, Qiyuan","last_name":"He"},{"first_name":"Xun","last_name":"Hong","full_name":"Hong, Xun"},{"last_name":"Hu","full_name":"Hu, Sheng","first_name":"Sheng"},{"first_name":"Weida","last_name":"Hu","full_name":"Hu, Weida"},{"first_name":"Wei","last_name":"Huang","full_name":"Huang, Wei"},{"first_name":"Yuan","last_name":"Huang","full_name":"Huang, Yuan"},{"last_name":"Ji","full_name":"Ji, Wei","first_name":"Wei"},{"last_name":"Li","full_name":"Li, Dehui","first_name":"Dehui"},{"first_name":"Lain Jong","last_name":"Li","full_name":"Li, Lain Jong"},{"first_name":"Qiang","last_name":"Li","full_name":"Li, Qiang"},{"last_name":"Lin","full_name":"Lin, Li","first_name":"Li"},{"first_name":"Chongyi","full_name":"Ling, Chongyi","last_name":"Ling"},{"full_name":"Liu, Minghua","last_name":"Liu","first_name":"Minghua"},{"last_name":"Liu","full_name":"Liu, Nan","first_name":"Nan"},{"last_name":"Liu","full_name":"Liu, Zhuang","first_name":"Zhuang"},{"full_name":"Loh, Kian Ping","last_name":"Loh","first_name":"Kian Ping"},{"full_name":"Ma, Jianmin","last_name":"Ma","first_name":"Jianmin"},{"full_name":"Miao, Feng","last_name":"Miao","first_name":"Feng"},{"last_name":"Peng","full_name":"Peng, Hailin","first_name":"Hailin"},{"first_name":"Mingfei","last_name":"Shao","full_name":"Shao, Mingfei"},{"last_name":"Song","full_name":"Song, Li","first_name":"Li"},{"first_name":"Shao","full_name":"Su, Shao","last_name":"Su"},{"full_name":"Sun, Shuo","last_name":"Sun","first_name":"Shuo"},{"first_name":"Chaoliang","full_name":"Tan, Chaoliang","last_name":"Tan"},{"full_name":"Tang, Zhiyong","last_name":"Tang","first_name":"Zhiyong"},{"last_name":"Wang","full_name":"Wang, Dingsheng","first_name":"Dingsheng"},{"first_name":"Huan","last_name":"Wang","full_name":"Wang, Huan"},{"first_name":"Jinlan","full_name":"Wang, Jinlan","last_name":"Wang"},{"first_name":"Xin","last_name":"Wang","full_name":"Wang, Xin"},{"first_name":"Xinran","last_name":"Wang","full_name":"Wang, Xinran"},{"first_name":"Andrew T.S.","full_name":"Wee, Andrew T.S.","last_name":"Wee"},{"first_name":"Zhongming","last_name":"Wei","full_name":"Wei, Zhongming"},{"first_name":"Yuen","last_name":"Wu","full_name":"Wu, Yuen"},{"last_name":"Wu","full_name":"Wu, Zhong Shuai","first_name":"Zhong Shuai"},{"first_name":"Jie","last_name":"Xiong","full_name":"Xiong, Jie"},{"last_name":"Xiong","full_name":"Xiong, Qihua","first_name":"Qihua"},{"first_name":"Weigao","full_name":"Xu, Weigao","last_name":"Xu"},{"first_name":"Peng","last_name":"Yin","full_name":"Yin, Peng"},{"full_name":"Zeng, Haibo","last_name":"Zeng","first_name":"Haibo"},{"first_name":"Zhiyuan","full_name":"Zeng, Zhiyuan","last_name":"Zeng"},{"full_name":"Zhai, Tianyou","last_name":"Zhai","first_name":"Tianyou"},{"last_name":"Zhang","full_name":"Zhang, Han","first_name":"Han"},{"last_name":"Zhang","full_name":"Zhang, Hui","first_name":"Hui"},{"first_name":"Qichun","full_name":"Zhang, Qichun","last_name":"Zhang"},{"first_name":"Tierui","full_name":"Zhang, Tierui","last_name":"Zhang"},{"first_name":"Xiang","last_name":"Zhang","full_name":"Zhang, Xiang"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"},{"first_name":"Meiting","full_name":"Zhao, Meiting","last_name":"Zhao"},{"full_name":"Zhao, Weijie","last_name":"Zhao","first_name":"Weijie"},{"full_name":"Zhao, Yunxuan","last_name":"Zhao","first_name":"Yunxuan"},{"last_name":"Zhou","full_name":"Zhou, Kai Ge","first_name":"Kai Ge"},{"last_name":"Zhou","full_name":"Zhou, Xing","first_name":"Xing"},{"first_name":"Yu","full_name":"Zhou, Yu","last_name":"Zhou"},{"full_name":"Zhu, Hongwei","last_name":"Zhu","first_name":"Hongwei"},{"full_name":"Zhang, Hua","last_name":"Zhang","first_name":"Hua"},{"first_name":"Zhongfan","last_name":"Liu","full_name":"Liu, Zhongfan"}],"status":"public","article_number":"2108017","oa":1,"date_created":"2024-01-14T23:00:58Z","citation":{"ieee":"C. Chang <i>et al.</i>, “Recent progress on two-dimensional materials,” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12. Peking University, 2021.","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017.","ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. 2021;37(12). doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>","mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12, 2108017, Peking University, 2021, doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>.","chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>. Peking University, 2021. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>.","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. Peking University. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>"},"quality_controlled":"1","title":"Recent progress on two-dimensional materials","volume":37,"day":"13","publication":"Acta Physico-Chimica Sinica","intvolume":"        37","date_published":"2021-10-13T00:00:00Z","doi":"10.3866/PKU.WHXB202108017","article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-02-05T10:02:45Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.02098","open_access":"1"}],"abstract":[{"lang":"eng","text":"We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2."}],"status":"public","author":[{"full_name":"Leopold, Nikolai K","last_name":"Leopold","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"},{"last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"publisher":"Mathematical Sciences Publishers","external_id":{"arxiv":["2005.02098"]},"publication_status":"published","issue":"4","_id":"14889","oa_version":"Preprint","type":"journal_article","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"year":"2021","month":"10","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"article_type":"original","department":[{"_id":"RoSe"}],"publication":"Pure and Applied Analysis","acknowledgement":"Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions.","day":"01","volume":3,"date_published":"2021-10-01T00:00:00Z","intvolume":"         3","doi":"10.2140/paa.2021.3.653","article_processing_charge":"No","ec_funded":1,"oa":1,"arxiv":1,"quality_controlled":"1","citation":{"ama":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. 2021;3(4):653-676. doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>","short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676.","ieee":"N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” <i>Pure and Applied Analysis</i>, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021.","ista":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676.","mla":"Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>.","apa":"Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &#38; Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>."},"date_created":"2024-01-28T23:01:43Z","page":"653-676","title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron"}]