[{"type":"preprint","_id":"7675","fulldoi":"https://doi.org/10.1101/2020.04.08.029405","title":"Normative models of enhancer function","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8155","status":"public"}]},"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"date_updated":"2026-07-06T12:43:43Z","oa_version":"Preprint","author":[{"first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","last_name":"Grah"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper"}],"year":"2020","article_processing_charge":"No","day":"09","citation":{"ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” <i>bioRxiv</i>. 2020.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Normative models of enhancer function. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” <i>BioRxiv</i>, 2020, doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, <a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” <i>BioRxiv</i>, 2020. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"bioRxiv","das_tickbox":"1","date_published":"2020-04-09T00:00:00Z","date_created":"2020-04-23T10:12:51Z","month":"04","corr_author":"1","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"oa":1,"external_id":{"biorxivid":["10.1101/2020.04.08.029405"]},"biorxivid":1,"project":[{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1101/2020.04.08.029405","language":[{"iso":"eng"}]},{"citation":{"ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>","ieee":"L. Santini <i>et al.</i>, “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” <i>bioRxiv</i>. ."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"05","pmid":1,"publication_status":"submitted","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"date_updated":"2026-07-06T12:45:07Z","oa_version":"Preprint","author":[{"last_name":"Santini","full_name":"Santini, Laura","first_name":"Laura"},{"last_name":"Halbritter","full_name":"Halbritter, Florian","first_name":"Florian"},{"last_name":"Titz-Teixeira","first_name":"Fabian","full_name":"Titz-Teixeira, Fabian"},{"last_name":"Suzuki","first_name":"Toru","full_name":"Suzuki, Toru"},{"first_name":"Maki","full_name":"Asami, Maki","last_name":"Asami"},{"last_name":"Ramesmayer","first_name":"Julia","full_name":"Ramesmayer, Julia"},{"first_name":"Xiaoyan","full_name":"Ma, Xiaoyan","last_name":"Ma"},{"full_name":"Lackner, Andreas","first_name":"Andreas","last_name":"Lackner"},{"last_name":"Warr","full_name":"Warr, Nick","first_name":"Nick"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"last_name":"Laue","first_name":"Ernest","full_name":"Laue, Ernest"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"last_name":"Beyer","full_name":"Beyer, Andreas","first_name":"Andreas"},{"first_name":"Anthony C. F.","full_name":"Perry, Anthony C. F.","last_name":"Perry"},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}],"year":"2020","type":"preprint","_id":"8813","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","fulldoi":"https://doi.org/10.1101/2020.11.03.366948","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"doi":"10.1101/2020.11.03.366948","abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"oa":1,"external_id":{"pmid":["PPR234457 "]},"month":"11","status":"public","publication":"bioRxiv","das_tickbox":"1","date_published":"2020-11-05T00:00:00Z","date_created":"2020-11-26T07:17:19Z"},{"language":[{"iso":"eng"}],"doi":"10.1101/791137","page":"22","oa":1,"abstract":[{"text":"Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals.","lang":"eng"}],"month":"02","date_published":"2020-02-19T00:00:00Z","date_created":"2020-03-21T16:34:42Z","publication":"bioRxiv","das_tickbox":"1","status":"public","citation":{"short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020).","mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>, 2020, doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>.","ieee":"Z. Wei <i>et al.</i>, “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” <i>bioRxiv</i>. 2020.","apa":"Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020). Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>","ista":"Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv, <a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>.","ama":"Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>","chicago":"Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen, Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>, 2020. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"19","main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"publication_status":"published","year":"2020","oa_version":"Preprint","author":[{"first_name":"Zhuang","full_name":"Wei, Zhuang","last_name":"Wei"},{"first_name":"Shutang","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"first_name":"Tao","full_name":"Liu, Tao","last_name":"Liu"},{"last_name":"Wu","first_name":"Yuan","full_name":"Wu, Yuan"},{"last_name":"Lei","first_name":"Ji-Gang","full_name":"Lei, Ji-Gang"},{"first_name":"ZhengJun","full_name":"Chen, ZhengJun","last_name":"Chen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Xue, Hong-Wei","first_name":"Hong-Wei","last_name":"Xue"},{"last_name":"Liao","full_name":"Liao, Kan","first_name":"Kan"}],"date_updated":"2026-07-06T12:53:37Z","title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","fulldoi":"https://doi.org/10.1101/791137","type":"preprint","_id":"7601","department":[{"_id":"JiFr"}]},{"date_published":"2020-06-01T00:00:00Z","publication":"Annales Scientifiques de l'Ecole Normale Superieure","quality_controlled":"1","abstract":[{"lang":"eng","text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions."},{"text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. ","lang":"fre"}],"publisher":"Societe Mathematique de France","intvolume":"        53","volume":53,"department":[{"_id":"TaHa"}],"scopus_import":"1","type":"journal_article","year":"2020","date_updated":"2026-07-06T13:57:35Z","author":[{"first_name":"C.","full_name":"Su, C.","last_name":"Su"},{"last_name":"Zhao","orcid":"0000-0001-7361-2882","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","full_name":"Zhao, Gufang"},{"last_name":"Zhong","full_name":"Zhong, C.","first_name":"C."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"isi":1,"article_processing_charge":"No","arxiv":1,"date_created":"2020-09-20T22:01:38Z","publication_identifier":{"issn":["0012-9593"]},"status":"public","das_tickbox":"1","month":"06","issue":"3","page":"663-671","external_id":{"isi":["000592182600004"],"arxiv":["1708.08013"]},"oa":1,"doi":"10.24033/asens.2431","language":[{"iso":"eng"}],"article_type":"original","title":"On the K-theory stable bases of the springer resolution","fulldoi":"https://doi.org/10.24033/asens.2431","_id":"8539","oa_version":"Preprint","publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. 2020;53(3):663-671. doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Societe Mathematique de France, 2020. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3, Societe Mathematique de France, 2020, pp. 663–71, doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3. Societe Mathematique de France, pp. 663–671, 2020.","apa":"Su, C., Zhao, G., &#38; Zhong, C. (2020). On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Societe Mathematique de France. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>"}},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Preprint","publication_status":"published","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","fulldoi":"https://doi.org/10.1137/19m126284x","_id":"9781","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>.","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(1):605-622. doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1. Society for Industrial and Applied Mathematics, pp. 605–622, 2020.","apa":"Feliciangeli, D., &#38; Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1, Society for Industrial and Applied Mathematics, 2020, pp. 605–22, doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>."},"ec_funded":1,"day":"12","month":"02","issue":"1","date_created":"2021-08-06T07:34:16Z","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"das_tickbox":"1","status":"public","language":[{"iso":"eng"}],"doi":"10.1137/19m126284x","article_type":"original","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"605-622","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"oa":1,"year":"2020","date_updated":"2026-07-06T14:02:25Z","author":[{"last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario","full_name":"Feliciangeli, Dario"},{"first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"isi":1,"department":[{"_id":"RoSe"}],"volume":52,"related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"}]},"type":"journal_article","scopus_import":"1","article_processing_charge":"No","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","arxiv":1,"corr_author":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","has_accepted_license":"1","ddc":["510"],"quality_controlled":"1","date_published":"2020-02-12T00:00:00Z","publication":"SIAM Journal on Mathematical Analysis","publisher":"Society for Industrial and Applied Mathematics","intvolume":"        52","abstract":[{"lang":"eng","text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum."}]},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"corr_author":"1","has_accepted_license":"1","ddc":["539"],"date_published":"2020-12-21T00:00:00Z","OA_place":"publisher","degree_awarded":"PhD","article_processing_charge":"No","year":"2020","date_updated":"2026-07-07T05:31:09Z","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Xiang","full_name":"Li, Xiang"}],"department":[{"_id":"MiLe"}],"related_material":{"record":[{"status":"public","id":"8587","relation":"part_of_dissertation"},{"status":"public","id":"1120","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5886"}]},"type":"dissertation","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8958","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"page":"125","oa":1,"month":"12","alternative_title":["ISTA Thesis"],"date_created":"2020-12-21T09:44:30Z","publication_identifier":{"issn":["2663-337X"]},"status":"public","file":[{"date_created":"2020-12-22T10:55:56Z","file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-12-22T10:55:56Z","content_type":"application/pdf","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"creator":"xli","file_size":3622305,"file_id":"8967"},{"date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip","access_level":"closed","date_updated":"2020-12-30T07:18:03Z","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"0954ecfc5554c05615c14de803341f00","file_size":4018859,"creator":"xli","file_id":"8968"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","mla":"Li, Xiang. <i>Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). <i>Rotation of coupled cold molecules in the presence of a many-body environment</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>"},"file_date_updated":"2020-12-30T07:18:03Z","ec_funded":1,"day":"21","oa_version":"Published Version","publication_status":"published","fulldoi":"https://doi.org/10.15479/AT:ISTA:8958","title":"Rotation of coupled cold molecules in the presence of a many-body environment","_id":"8958"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: <i>34th International Symposium on Distributed Computing</i>. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">10.4230/LIPIcs.DISC.2020.40</a>","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In <i>34th International Symposium on Distributed Computing</i>, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">https://doi.org/10.4230/LIPIcs.DISC.2020.40</a>.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” <i>34th International Symposium on Distributed Computing</i>, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">10.4230/LIPIcs.DISC.2020.40</a>.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., &#38; Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In <i>34th International Symposium on Distributed Computing</i> (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.40\">https://doi.org/10.4230/LIPIcs.DISC.2020.40</a>","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in <i>34th International Symposium on Distributed Computing</i>, Virtual, 2020, vol. 179."},"file_date_updated":"2024-03-05T07:08:27Z","day":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"oa_version":"Published Version","publication_status":"published","fulldoi":"https://doi.org/10.4230/LIPIcs.DISC.2020.40","title":"Brief announcement: Efficient load-balancing through distributed token dropping","article_number":"40","_id":"15074","doi":"10.4230/LIPIcs.DISC.2020.40","language":[{"iso":"eng"}],"external_id":{"arxiv":["2005.07761"]},"oa":1,"month":"10","alternative_title":["LIPIcs"],"date_created":"2024-03-05T07:09:12Z","status":"public","file":[{"date_created":"2024-03-05T07:08:27Z","access_level":"open_access","file_name":"2020_LIPIcs_Brandt.pdf","date_updated":"2024-03-05T07:08:27Z","relation":"main_file","content_type":"application/pdf","checksum":"23e2d9321aef53092dc1e24a8ab82d72","file_size":303529,"creator":"dernst","success":1,"file_id":"15075"}],"article_processing_charge":"No","arxiv":1,"year":"2020","date_updated":"2026-07-07T06:21:32Z","author":[{"last_name":"Brandt","full_name":"Brandt, Sebastian","first_name":"Sebastian"},{"full_name":"Keller, Barbara","first_name":"Barbara","last_name":"Keller"},{"first_name":"Joel","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Suomela, Jukka","first_name":"Jukka","last_name":"Suomela"},{"full_name":"Uitto, Jara","first_name":"Jara","last_name":"Uitto"}],"volume":179,"related_material":{"record":[{"relation":"later_version","status":"public","id":"9678"}]},"department":[{"_id":"DaAl"}],"scopus_import":"1","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       179","conference":{"name":"DISC: Symposium on Distributed Computing","end_date":"2020-10-16","start_date":"2020-10-12","location":"Virtual"},"abstract":[{"text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.","lang":"eng"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by/3.0/","has_accepted_license":"1","ddc":["000"],"quality_controlled":"1","date_published":"2020-10-07T00:00:00Z","publication":"34th International Symposium on Distributed Computing"},{"conference":{"start_date":"2020-07-12","location":"Online","name":"ICML: International Conference on Machine Learning","end_date":"2020-07-18"},"intvolume":"       119","abstract":[{"text":"Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost. ","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","ddc":["000"],"publication":"37th International Conference on Machine Learning","date_published":"2020-07-12T00:00:00Z","article_processing_charge":"No","date_updated":"2026-07-07T13:42:32Z","author":[{"first_name":"Mark","full_name":"Kurtz, Mark","last_name":"Kurtz"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"last_name":"Matveev","full_name":"Matveev, Alexander","first_name":"Alexander"},{"full_name":"Carr, John","first_name":"John","last_name":"Carr"},{"full_name":"Goin, Michael","first_name":"Michael","last_name":"Goin"},{"last_name":"Leiserson","first_name":"William","full_name":"Leiserson, William"},{"first_name":"Sage","full_name":"Moore, Sage","last_name":"Moore"},{"full_name":"Nell, Bill","first_name":"Bill","last_name":"Nell"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"year":"2020","department":[{"_id":"DaAl"}],"volume":119,"scopus_import":"1","type":"conference","language":[{"iso":"eng"}],"oa":1,"page":"5533-5543","month":"07","status":"public","das_tickbox":"1","publication_identifier":{"issn":["2640-3498"]},"date_created":"2021-05-23T22:01:45Z","file":[{"creator":"kschuh","success":1,"file_size":741899,"file_id":"9421","checksum":"2aaaa7d7226e49161311d91627cf783b","date_updated":"2021-05-25T09:51:36Z","relation":"main_file","content_type":"application/pdf","date_created":"2021-05-25T09:51:36Z","file_name":"2020_PMLR_Kurtz.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kurtz M, Kopinsky J, Gelashvili R, Matveev A, Carr J, Goin M, Leiserson W, Moore S, Nell B, Shavit N, Alistarh D-A. 2020. Inducing and exploiting activation sparsity for fast neural network inference. 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5533–5543.","ama":"Kurtz M, Kopinsky J, Gelashvili R, et al. Inducing and exploiting activation sparsity for fast neural network inference. In: <i>37th International Conference on Machine Learning</i>. Vol 119. ; 2020:5533-5543.","chicago":"Kurtz, Mark, Justin Kopinsky, Rati Gelashvili, Alexander Matveev, John Carr, Michael Goin, William Leiserson, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” In <i>37th International Conference on Machine Learning</i>, 119:5533–43, 2020.","ieee":"M. Kurtz <i>et al.</i>, “Inducing and exploiting activation sparsity for fast neural network inference,” in <i>37th International Conference on Machine Learning</i>, Online, 2020, vol. 119, pp. 5533–5543.","apa":"Kurtz, M., Kopinsky, J., Gelashvili, R., Matveev, A., Carr, J., Goin, M., … Alistarh, D.-A. (2020). Inducing and exploiting activation sparsity for fast neural network inference. In <i>37th International Conference on Machine Learning</i> (Vol. 119, pp. 5533–5543). Online.","short":"M. Kurtz, J. Kopinsky, R. Gelashvili, A. Matveev, J. Carr, M. Goin, W. Leiserson, S. Moore, B. Nell, N. Shavit, D.-A. Alistarh, in:, 37th International Conference on Machine Learning, 2020, pp. 5533–5543.","mla":"Kurtz, Mark, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” <i>37th International Conference on Machine Learning</i>, vol. 119, 2020, pp. 5533–43."},"file_date_updated":"2021-05-25T09:51:36Z","day":"12","oa_version":"Published Version","_id":"9415","title":"Inducing and exploiting activation sparsity for fast neural network inference"},{"type":"journal_article","scopus_import":"1","volume":125,"department":[{"_id":"OnHo"}],"main_file_link":[{"url":"https://arxiv.org/abs/1912.10218","open_access":"1"}],"isi":1,"year":"2020","date_updated":"2026-07-08T08:56:44Z","author":[{"last_name":"Malia","first_name":"Benjamin K.","full_name":"Malia, Benjamin K."},{"last_name":"Martínez-Rincón","first_name":"Julián","full_name":"Martínez-Rincón, Julián"},{"last_name":"Wu","full_name":"Wu, Yunfan","first_name":"Yunfan"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","last_name":"Hosten","full_name":"Hosten, Onur","first_name":"Onur"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"article_processing_charge":"No","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","arxiv":1,"date_published":"2020-07-24T00:00:00Z","publication":"Physical Review Letters","quality_controlled":"1","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"intvolume":"       125","publisher":"American Physical Society","article_number":"043202","fulldoi":"https://doi.org/10.1103/PhysRevLett.125.043202","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","_id":"8285","publication_status":"published","pmid":1,"oa_version":"Preprint","day":"24","citation":{"ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>.","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. 2020;125(4). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” <i>Physical Review Letters</i>, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">10.1103/PhysRevLett.125.043202</a>.","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” <i>Physical Review Letters</i>, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., &#38; Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.043202\">https://doi.org/10.1103/PhysRevLett.125.043202</a>"},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","supplementarymaterial":"yes","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2020-08-24T06:24:04Z","das_tickbox":"0","status":"public","issue":"4","month":"07","external_id":{"pmid":["32794788"],"isi":["000552227400008"],"arxiv":["1912.10218"]},"oa":1,"researchdata_availability":"no","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.125.043202","article_type":"original"},{"publication_status":"published","oa_version":"Preprint","_id":"8319","fulldoi":"https://doi.org/10.1103/PhysRevA.102.012224","article_number":"012224","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","citation":{"ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. <i>Physical Review A</i>. 2020;102(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">10.1103/PhysRevA.102.012224</a>","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” <i>Physical Review A</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">https://doi.org/10.1103/PhysRevA.102.012224</a>.","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” <i>Physical Review A</i>, vol. 102, no. 1. American Physical Society, 2020.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., &#38; Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">https://doi.org/10.1103/PhysRevA.102.012224</a>","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” <i>Physical Review A</i>, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevA.102.012224\">10.1103/PhysRevA.102.012224</a>.","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020)."},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","day":"30","issue":"1","month":"07","supplementarymaterial":"no","das_tickbox":"0","status":"public","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"date_created":"2020-08-30T22:01:10Z","doi":"10.1103/PhysRevA.102.012224","article_type":"original","language":[{"iso":"eng"}],"oa":1,"researchdata_availability":"no","external_id":{"arxiv":["1912.08334"],"isi":["000555104200011"]},"isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08334"}],"date_updated":"2026-07-08T08:59:02Z","author":[{"last_name":"Wu","full_name":"Wu, Yunfan","first_name":"Yunfan"},{"last_name":"Krishnakumar","full_name":"Krishnakumar, Rajiv","first_name":"Rajiv"},{"full_name":"Martínez-Rincón, Julián","first_name":"Julián","last_name":"Martínez-Rincón"},{"last_name":"Malia","full_name":"Malia, Benjamin K.","first_name":"Benjamin K."},{"first_name":"Onur","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kasevich, Mark A.","first_name":"Mark A.","last_name":"Kasevich"}],"year":"2020","type":"journal_article","scopus_import":"1","volume":102,"department":[{"_id":"OnHo"}],"arxiv":1,"acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","article_processing_charge":"No","quality_controlled":"1","publication":"Physical Review A","date_published":"2020-07-30T00:00:00Z","intvolume":"       102","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated."}]},{"month":"09","date_created":"2020-07-16T12:26:04Z","publication_identifier":{"eissn":["2050-084X"]},"status":"public","das_tickbox":"1","file":[{"relation":"main_file","date_updated":"2020-10-27T11:37:32Z","content_type":"application/pdf","date_created":"2020-10-27T11:37:32Z","file_name":"2020_eLife_Gonçalves.pdf","access_level":"open_access","creator":"cziletti","success":1,"file_size":17355867,"file_id":"8709","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be"}],"doi":"10.7554/eLife.56261","language":[{"iso":"eng"}],"article_type":"original","project":[{"grant_number":"819603","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"external_id":{"isi":["000584989400001"],"pmid":["32940606"]},"oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"publication_status":"published","fulldoi":"https://doi.org/10.7554/eLife.56261","article_number":"e56261","title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","_id":"8127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-10-27T11:37:32Z","ec_funded":1,"citation":{"chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.56261\">https://doi.org/10.7554/eLife.56261</a>.","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.56261\">10.7554/eLife.56261</a>","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261.","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” <i>ELife</i>, vol. 9, e56261, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.56261\">10.7554/eLife.56261</a>.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.56261\">https://doi.org/10.7554/eLife.56261</a>","ieee":"P. J. Gonçalves <i>et al.</i>, “Training deep neural density estimators to identify mechanistic models of neural dynamics,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"day":"17","has_accepted_license":"1","ddc":["570"],"quality_controlled":"1","date_published":"2020-09-17T00:00:00Z","publication":"eLife","publisher":"eLife Sciences Publications","intvolume":"         9","abstract":[{"text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"year":"2020","author":[{"first_name":"Pedro J.","full_name":"Gonçalves, Pedro J.","last_name":"Gonçalves","orcid":"0000-0002-6987-4836"},{"full_name":"Lueckmann, Jan-Matthis","first_name":"Jan-Matthis","orcid":"0000-0003-4320-4663","last_name":"Lueckmann"},{"orcid":"0000-0002-3573-0404","last_name":"Deistler","first_name":"Michael","full_name":"Deistler, Michael"},{"first_name":"Marcel","full_name":"Nonnenmacher, Marcel","orcid":"0000-0001-6044-6627","last_name":"Nonnenmacher"},{"last_name":"Öcal","orcid":"0000-0002-8528-6858","first_name":"Kaan","full_name":"Öcal, Kaan"},{"first_name":"Giacomo","full_name":"Bassetto, Giacomo","last_name":"Bassetto"},{"id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","orcid":"0000-0003-4252-1608","last_name":"Chintaluri","first_name":"Chaitanya","full_name":"Chintaluri, Chaitanya"},{"orcid":"0000-0001-6619-7502","last_name":"Podlaski","full_name":"Podlaski, William F.","first_name":"William F."},{"orcid":"0000-0003-0807-0823","last_name":"Haddad","first_name":"Sara A.","full_name":"Haddad, Sara A."},{"first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Greenberg","full_name":"Greenberg, David S.","first_name":"David S."},{"last_name":"Macke","orcid":"0000-0001-5154-8912","first_name":"Jakob H.","full_name":"Macke, Jakob H."}],"date_updated":"2026-07-13T12:31:21Z","isi":1,"volume":9,"department":[{"_id":"TiVo"}],"scopus_import":"1","type":"journal_article","acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","article_processing_charge":"No"},{"intvolume":"         3","publisher":"American Chemical Society","abstract":[{"text":"Nanomaterials produced from the bottom-up assembly of nanocrystals may incorporate ∼1020–1021 cm–3 not fully coordinated surface atoms, i.e., ∼1020–1021 cm–3 potential donor or acceptor states that can strongly affect transport properties. Therefore, to exploit the full potential of nanocrystal building blocks to produce functional nanomaterials and thin films, a proper control of their surface chemistry is required. Here, we analyze how the ligand stripping procedure influences the charge and heat transport properties of sintered PbSe nanomaterials produced from the bottom-up assembly of colloidal PbSe nanocrystals. First, we show that the removal of the native organic ligands by thermal decomposition in an inert atmosphere leaves relatively large amounts of carbon at the crystal interfaces. This carbon blocks crystal growth during consolidation and at the same time hampers charge and heat transport through the final nanomaterial. Second, we demonstrate that, by stripping ligands from the nanocrystal surface before consolidation, nanomaterials with larger crystal domains, lower porosity, and higher charge carrier concentrations are obtained, thus resulting in nanomaterials with higher electrical and thermal conductivities. In addition, the ligand displacement leaves the nanocrystal surface unprotected, facilitating oxidation and chalcogen evaporation. The influence of the ligand displacement on the nanomaterial charge transport properties is rationalized here using a two-band model based on the standard Boltzmann transport equation with the relaxation time approximation. Finally, we present an application of the produced functional nanomaterials by modeling, fabricating, and testing a simple PbSe-based thermoelectric device with a ring geometry.","lang":"eng"}],"ddc":["540"],"quality_controlled":"1","has_accepted_license":"1","date_published":"2020-03-01T00:00:00Z","publication":"ACS Applied Energy Materials","article_processing_charge":"No","acknowledgement":"This work was supported by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP (ENE2016-77798-C4-3-R) and the Generalitat de Catalunya through the project 2017SGR1246. D.C. acknowledges support from Universidad Nacional de Colombia. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 754411. M.I. acknowledges financial support from IST Austria.","isi":1,"year":"2020","author":[{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"first_name":"Silvia","full_name":"Ortega, Silvia","last_name":"Ortega"},{"first_name":"Sergio","full_name":"Illera, Sergio","last_name":"Illera"},{"orcid":"0000-0001-7313-6740","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","full_name":"Liu, Yu"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shavel","full_name":"Shavel, Alexey","first_name":"Alexey"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"full_name":"López, Antonio M.","first_name":"Antonio M.","last_name":"López"},{"last_name":"Noriega","full_name":"Noriega, Germán","first_name":"Germán"},{"last_name":"Durá","full_name":"Durá, Oscar Juan","first_name":"Oscar Juan"},{"full_name":"López De La Torre, M. A.","first_name":"M. A.","last_name":"López De La Torre"},{"full_name":"Prades, Joan Daniel","first_name":"Joan Daniel","last_name":"Prades"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_updated":"2026-07-28T12:54:00Z","scopus_import":"1","type":"journal_article","department":[{"_id":"MaIb"}],"volume":3,"language":[{"iso":"eng"}],"doi":"10.1021/acsaem.9b02137","article_type":"original","external_id":{"isi":["000526598300012"]},"page":"2120-2129","oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"issue":"3","month":"03","file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2022-08-23T08:34:17Z","access_level":"open_access","file_name":"2020_ACSAppliedEnergyMat_Cadavid.pdf","date_created":"2022-08-23T08:34:17Z","file_id":"11942","file_size":6423548,"success":1,"creator":"dernst","checksum":"f23be731a766a480c77c962c1380315c"}],"date_created":"2020-02-09T23:00:52Z","publication_identifier":{"eissn":["2574-0962"]},"status":"public","file_date_updated":"2022-08-23T08:34:17Z","ec_funded":1,"citation":{"ieee":"D. Cadavid <i>et al.</i>, “Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials,” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3. American Chemical Society, pp. 2120–2129, 2020.","apa":"Cadavid, D., Ortega, S., Illera, S., Liu, Y., Ibáñez, M., Shavel, A., … Cabot, A. (2020). Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>","short":"D. Cadavid, S. Ortega, S. Illera, Y. Liu, M. Ibáñez, A. Shavel, Y. Zhang, M. Li, A.M. López, G. Noriega, O.J. Durá, M.A. López De La Torre, J.D. Prades, A. Cabot, ACS Applied Energy Materials 3 (2020) 2120–2129.","mla":"Cadavid, Doris, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>, vol. 3, no. 3, American Chemical Society, 2020, pp. 2120–29, doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>.","ista":"Cadavid D, Ortega S, Illera S, Liu Y, Ibáñez M, Shavel A, Zhang Y, Li M, López AM, Noriega G, Durá OJ, López De La Torre MA, Prades JD, Cabot A. 2020. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. ACS Applied Energy Materials. 3(3), 2120–2129.","chicago":"Cadavid, Doris, Silvia Ortega, Sergio Illera, Yu Liu, Maria Ibáñez, Alexey Shavel, Yu Zhang, et al. “Influence of the Ligand Stripping on the Transport Properties of Nanoparticle-Based PbSe Nanomaterials.” <i>ACS Applied Energy Materials</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acsaem.9b02137\">https://doi.org/10.1021/acsaem.9b02137</a>.","ama":"Cadavid D, Ortega S, Illera S, et al. Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials. <i>ACS Applied Energy Materials</i>. 2020;3(3):2120-2129. doi:<a href=\"https://doi.org/10.1021/acsaem.9b02137\">10.1021/acsaem.9b02137</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","OA_type":"green","oa_version":"Accepted Version","fulldoi":"https://doi.org/10.1021/acsaem.9b02137","title":"Influence of the ligand stripping on the transport properties of nanoparticle-based PbSe nanomaterials","_id":"7467"},{"title":"Novel insights into PIN polarity regulation during Arabidopsis development","fulldoi":"https://doi.org/10.15479/AT:ISTA:8589","_id":"8589","oa_version":"Published Version","publication_status":"published","day":"30","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","apa":"Han, H. (2020). <i>Novel insights into PIN polarity regulation during Arabidopsis development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>","mla":"Han, Huibin. <i>Novel Insights into PIN Polarity Regulation during Arabidopsis Development</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>."},"file_date_updated":"2021-10-01T13:33:02Z","date_created":"2020-09-30T14:50:51Z","publication_identifier":{"issn":["2663-337X"]},"status":"public","file":[{"file_name":"2020_Han_Thesis.docx","access_level":"closed","date_created":"2020-09-30T14:50:20Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","date_updated":"2020-09-30T14:50:20Z","checksum":"c4bda1947d4c09c428ac9ce667b02327","file_id":"8590","creator":"dernst","file_size":49198118},{"file_name":"2020_Han_Thesis.pdf","access_level":"open_access","date_created":"2020-09-30T14:49:59Z","content_type":"application/pdf","date_updated":"2021-10-01T13:33:02Z","relation":"main_file","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","file_id":"8591","file_size":15513963,"creator":"dernst"}],"month":"09","alternative_title":["ISTA Thesis"],"page":"164","oa":1,"doi":"10.15479/AT:ISTA:8589","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7643","status":"public"}]},"department":[{"_id":"JiFr"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"type":"dissertation","year":"2020","date_updated":"2026-07-28T12:51:58Z","author":[{"first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han"}],"acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","article_processing_charge":"No","degree_awarded":"PhD","date_published":"2020-09-30T00:00:00Z","OA_place":"publisher","corr_author":"1","has_accepted_license":"1","ddc":["580"],"abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"}]},{"department":[{"_id":"KrPi"}],"volume":12171,"scopus_import":"1","type":"conference","year":"2020","date_updated":"2026-07-28T12:45:44Z","author":[{"id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","first_name":"Suvradip"},{"first_name":"Stefan","full_name":"Dziembowski, Stefan","last_name":"Dziembowski"},{"last_name":"Nielsen","full_name":"Nielsen, Jesper Buus","first_name":"Jesper Buus"}],"main_file_link":[{"url":"https://eprint.iacr.org/2019/1317","open_access":"1"}],"isi":1,"article_processing_charge":"No","acknowledgement":"We would like to thank the anonymous reviewers for their helpful comments and suggestions. The work was initiated while the first author was in IIT Madras, India. Part of this work was done while the author was visiting the University of Warsaw. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT) and from the Foundation for Polish Science under grant TEAM/2016-1/4 founded within the UE 2014–2020 Smart Growth Operational Program. The last author was supported by the Independent Research Fund Denmark project BETHE and the Concordium Blockchain Research Center, Aarhus University, Denmark.","date_published":"2020-08-10T00:00:00Z","OA_place":"repository","publication":"Advances in Cryptology – CRYPTO 2020","quality_controlled":"1","abstract":[{"text":"Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.\r\nIn this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.\r\nOur core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).","lang":"eng"}],"publisher":"Springer Nature","conference":{"end_date":"2020-08-21","name":"CRYPTO: Annual International Cryptology Conference","location":"Santa Barbara, CA, United States","start_date":"2020-08-17"},"intvolume":"     12171","fulldoi":"https://doi.org/10.1007/978-3-030-56880-1_26","cryptoeprintid":1,"title":"Reverse firewalls for actively secure MPCs","_id":"8322","oa_version":"Preprint","OA_type":"green","publication_status":"published","day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Actively Secure MPCs.” <i>Advances in Cryptology – CRYPTO 2020</i>, vol. 12171, Springer Nature, 2020, pp. 732–62, doi:<a href=\"https://doi.org/10.1007/978-3-030-56880-1_26\">10.1007/978-3-030-56880-1_26</a>.","short":"S. Chakraborty, S. Dziembowski, J.B. Nielsen, in:, Advances in Cryptology – CRYPTO 2020, Springer Nature, 2020, pp. 732–762.","ieee":"S. Chakraborty, S. Dziembowski, and J. B. Nielsen, “Reverse firewalls for actively secure MPCs,” in <i>Advances in Cryptology – CRYPTO 2020</i>, Santa Barbara, CA, United States, 2020, vol. 12171, pp. 732–762.","apa":"Chakraborty, S., Dziembowski, S., &#38; Nielsen, J. B. (2020). Reverse firewalls for actively secure MPCs. In <i>Advances in Cryptology – CRYPTO 2020</i> (Vol. 12171, pp. 732–762). Santa Barbara, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-56880-1_26\">https://doi.org/10.1007/978-3-030-56880-1_26</a>","ista":"Chakraborty S, Dziembowski S, Nielsen JB. 2020. Reverse firewalls for actively secure MPCs. Advances in Cryptology – CRYPTO 2020. CRYPTO: Annual International Cryptology Conference, LNCS, vol. 12171, 732–762.","ama":"Chakraborty S, Dziembowski S, Nielsen JB. Reverse firewalls for actively secure MPCs. In: <i>Advances in Cryptology – CRYPTO 2020</i>. Vol 12171. Springer Nature; 2020:732-762. doi:<a href=\"https://doi.org/10.1007/978-3-030-56880-1_26\">10.1007/978-3-030-56880-1_26</a>","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, and Jesper Buus Nielsen. “Reverse Firewalls for Actively Secure MPCs.” In <i>Advances in Cryptology – CRYPTO 2020</i>, 12171:732–62. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-56880-1_26\">https://doi.org/10.1007/978-3-030-56880-1_26</a>."},"ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030568795"],"issn":["0302-9743"]},"date_created":"2020-08-30T22:01:12Z","status":"public","month":"08","alternative_title":["LNCS"],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"732-762","external_id":{"isi":["001415325700026"],"cryptoeprintid":["2019/1317"]},"oa":1,"doi":"10.1007/978-3-030-56880-1_26","language":[{"iso":"eng"}]},{"day":"19","citation":{"short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2020, pp. 276–91, doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Diego, CA, United States, 2020, pp. 276–291.","apa":"Brown, T. A., Prokopec, A., &#38; Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 276–91. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>.","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2020:276-291. doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>"},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7636","fulldoi":"https://doi.org/10.1145/3332466.3374542","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","publication_status":"published","OA_type":"free access","oa_version":"Published Version","oa":1,"page":"276-291","external_id":{"isi":["000564476500020"]},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"language":[{"iso":"eng"}],"doi":"10.1145/3332466.3374542","status":"public","date_created":"2020-04-05T22:00:49Z","publication_identifier":{"isbn":["9781450368186"]},"month":"02","article_processing_charge":"No","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","scopus_import":"1","type":"conference","department":[{"_id":"DaAl"}],"isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"date_updated":"2026-07-28T12:49:59Z","author":[{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A","full_name":"Brown, Trevor A"},{"first_name":"Aleksandar","full_name":"Prokopec, Aleksandar","last_name":"Prokopec"},{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"year":"2020","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"conference":{"end_date":"2020-02-26","name":"PPOPP: Principles and Practice of Parallel Programming","location":"San Diego, CA, United States","start_date":"2020-02-22"},"publisher":"Association for Computing Machinery","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2020-02-19T00:00:00Z","OA_place":"publisher","quality_controlled":"1","ddc":["000"]},{"fulldoi":"https://doi.org/10.1016/j.neuron.2020.01.015","title":"Replay of behavioral sequences in the medial prefrontal cortex during rule switching","_id":"7472","publication_status":"published","OA_type":"free access","pmid":1,"oa_version":"Published Version","day":"08","citation":{"chicago":"Käfer, Karola, Michele Nardin, Karel Blahna, and Jozsef L Csicsvari. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>.","ama":"Käfer K, Nardin M, Blahna K, Csicsvari JL. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. 2020;106(1):P154-165.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>","ista":"Käfer K, Nardin M, Blahna K, Csicsvari JL. 2020. Replay of behavioral sequences in the medial prefrontal cortex during rule switching. Neuron. 106(1), P154–165.e6.","short":"K. Käfer, M. Nardin, K. Blahna, J.L. Csicsvari, Neuron 106 (2020) P154–165.e6.","mla":"Käfer, Karola, et al. “Replay of Behavioral Sequences in the Medial Prefrontal Cortex during Rule Switching.” <i>Neuron</i>, vol. 106, no. 1, Elsevier, 2020, p. P154–165.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">10.1016/j.neuron.2020.01.015</a>.","apa":"Käfer, K., Nardin, M., Blahna, K., &#38; Csicsvari, J. L. (2020). Replay of behavioral sequences in the medial prefrontal cortex during rule switching. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.015\">https://doi.org/10.1016/j.neuron.2020.01.015</a>","ieee":"K. Käfer, M. Nardin, K. Blahna, and J. L. Csicsvari, “Replay of behavioral sequences in the medial prefrontal cortex during rule switching,” <i>Neuron</i>, vol. 106, no. 1. Elsevier, p. P154–165.e6, 2020."},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-02-10T15:45:48Z","publication_identifier":{"issn":["0896-6273"]},"status":"public","issue":"1","month":"04","page":"P154-165.e6","external_id":{"pmid":["32032512"],"isi":["000525319300016"]},"oa":1,"project":[{"name":"inter-and intracellular signalling in schizophrenia","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"607616"}],"article_type":"original","doi":"10.1016/j.neuron.2020.01.015","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"scopus_import":"1","type":"journal_article","volume":106,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/this-brain-area-helps-us-decide/"}]},"department":[{"_id":"JoCs"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.015","open_access":"1"}],"isi":1,"year":"2020","date_updated":"2026-07-28T12:55:10Z","author":[{"last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","first_name":"Karola","full_name":"Käfer, Karola"},{"first_name":"Michele","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karel","full_name":"Blahna, Karel","id":"3EA859AE-F248-11E8-B48F-1D18A9856A87","last_name":"Blahna"},{"first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Todor Asenov and Thomas Menner from the Machine Shop for the drive design and production, Hugo Malagon-Vina for assistance in maze automatization, Jago Wallenschus for taking the images of the histology, and Federico Stella and Juan Felipe Ramirez-Villegas for comments on an earlier version of the manuscript. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616 ).","article_processing_charge":"No","OA_place":"publisher","date_published":"2020-04-08T00:00:00Z","publication":"Neuron","ddc":["570"],"quality_controlled":"1","corr_author":"1","abstract":[{"lang":"eng","text":"Temporally organized reactivation of experiences during awake immobility periods is thought to underlie cognitive processes like planning and evaluation. While replay of trajectories is well established for the hippocampus, it is unclear whether the medial prefrontal cortex (mPFC) can reactivate sequential behavioral experiences in the awake state to support task execution. We simultaneously recorded from hippocampal and mPFC principal neurons in rats performing a mPFC-dependent rule-switching task on a plus maze. We found that mPFC neuronal activity encoded relative positions between the start and goal. During awake immobility periods, the mPFC replayed temporally organized sequences of these generalized positions, resembling entire spatial trajectories. The occurrence of mPFC trajectory replay positively correlated with rule-switching performance. However, hippocampal and mPFC trajectory replay occurred independently, indicating different functions. These results demonstrate that the mPFC can replay ordered activity patterns representing generalized locations and suggest that mPFC replay might have a role in flexible behavior."}],"intvolume":"       106","publisher":"Elsevier"},{"article_processing_charge":"No","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship).  We thank Keiko U. Torii (University of Washington/Nagoya University), Mark Estelle (University of California San Diego), Ottoline Leyser (Sainsbury Laboratory, University of Cambridge), and Yunde Zhao (University of California San Diego) for sharing published genetic lines. We also thank Dr. Maciek Adamowski (Institute of Science and Technology Austria) for critical reading of the manuscript.","main_file_link":[{"url":"https://doi.org/10.1104/pp.20.00212","open_access":"1"}],"isi":1,"year":"2020","author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova","full_name":"Rakusova, Hana","first_name":"Hana"},{"full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"first_name":"Yuzhou","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"}],"date_updated":"2026-07-28T12:51:59Z","scopus_import":"1","type":"journal_article","related_material":{"record":[{"id":"8589","status":"public","relation":"dissertation_contains"}]},"volume":183,"department":[{"_id":"JiFr"}],"intvolume":"       183","publisher":"American Society of Plant Biologists","ddc":["580"],"quality_controlled":"1","corr_author":"1","date_published":"2020-05-08T00:00:00Z","OA_place":"publisher","publication":"Plant Physiology","citation":{"chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1104/pp.20.00212\">https://doi.org/10.1104/pp.20.00212</a>.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. <i>Plant Physiology</i>. 2020;183(5):37-40. doi:<a href=\"https://doi.org/10.1104/pp.20.00212\">10.1104/pp.20.00212</a>","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40.","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., &#38; Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.20.00212\">https://doi.org/10.1104/pp.20.00212</a>","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” <i>Plant Physiology</i>, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” <i>Plant Physiology</i>, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:<a href=\"https://doi.org/10.1104/pp.20.00212\">10.1104/pp.20.00212</a>."},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","pmid":1,"publication_status":"published","OA_type":"free access","oa_version":"Published Version","title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","fulldoi":"https://doi.org/10.1104/pp.20.00212","_id":"7643","article_type":"letter_editor","doi":"10.1104/pp.20.00212","language":[{"iso":"eng"}],"page":"37-40","external_id":{"isi":["000536641800018"],"pmid":["32107280"]},"oa":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"issue":"5","month":"05","date_created":"2020-04-06T10:06:40Z","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"status":"public"},{"type":"conference","scopus_import":"1","department":[{"_id":"GradSch"}],"isi":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02860087/document","open_access":"1"}],"author":[{"last_name":"Baig","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad"},{"full_name":"Hendler, Danny","first_name":"Danny","last_name":"Hendler"},{"last_name":"Milani","first_name":"Alessia","full_name":"Milani, Alessia"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}],"date_updated":"2026-07-28T09:50:30Z","year":"2020","article_processing_charge":"No","publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","date_published":"2020-07-31T00:00:00Z","quality_controlled":"1","abstract":[{"text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.","lang":"eng"}],"conference":{"start_date":"2020-08-03","location":"Virtual, Italy","name":"PODC: Principles of Distributed Computing","end_date":"2020-08-07"},"publisher":"Association for Computing Machinery","_id":"8382","fulldoi":"https://doi.org/10.1145/3382734.3406005","title":"Long-lived snapshots with polylogarithmic amortized step complexity","publication_status":"published","oa_version":"Preprint","day":"31","citation":{"ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, 31–40. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3382734.3406005\">https://doi.org/10.1145/3382734.3406005</a>.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2020:31-40. doi:<a href=\"https://doi.org/10.1145/3382734.3406005\">10.1145/3382734.3406005</a>","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2020, pp. 31–40.","apa":"Baig, M. A., Hendler, D., Milani, A., &#38; Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i> (pp. 31–40). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3382734.3406005\">https://doi.org/10.1145/3382734.3406005</a>","mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2020, pp. 31–40, doi:<a href=\"https://doi.org/10.1145/3382734.3406005\">10.1145/3382734.3406005</a>.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","das_tickbox":"1","publication_identifier":{"isbn":["9781450375825"]},"date_created":"2020-09-13T22:01:17Z","month":"07","oa":1,"external_id":{"isi":["001436693500004"]},"page":"31-40","doi":"10.1145/3382734.3406005","language":[{"iso":"eng"}]},{"_id":"6952","title":"Learning single-image 3D reconstruction by generative modelling of shape, pose and shading","fulldoi":"https://doi.org/10.1007/s11263-019-01219-8","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","OA_type":"hybrid","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:46Z","citation":{"ieee":"P. M. Henderson and V. Ferrari, “Learning single-image 3D reconstruction by generative modelling of shape, pose and shading,” <i>International Journal of Computer Vision</i>, vol. 128. Springer Nature, pp. 835–854, 2020.","apa":"Henderson, P. M., &#38; Ferrari, V. (2020). Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-019-01219-8\">https://doi.org/10.1007/s11263-019-01219-8</a>","short":"P.M. Henderson, V. Ferrari, International Journal of Computer Vision 128 (2020) 835–854.","mla":"Henderson, Paul M., and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” <i>International Journal of Computer Vision</i>, vol. 128, Springer Nature, 2020, pp. 835–54, doi:<a href=\"https://doi.org/10.1007/s11263-019-01219-8\">10.1007/s11263-019-01219-8</a>.","ista":"Henderson PM, Ferrari V. 2020. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 128, 835–854.","ama":"Henderson PM, Ferrari V. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. <i>International Journal of Computer Vision</i>. 2020;128:835-854. doi:<a href=\"https://doi.org/10.1007/s11263-019-01219-8\">10.1007/s11263-019-01219-8</a>","chicago":"Henderson, Paul M, and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” <i>International Journal of Computer Vision</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11263-019-01219-8\">https://doi.org/10.1007/s11263-019-01219-8</a>."},"status":"public","date_created":"2019-10-17T13:38:20Z","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"file":[{"file_name":"2019_CompVision_Henderson.pdf","access_level":"open_access","date_created":"2019-10-25T10:28:29Z","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","checksum":"a0f05dd4f5f64e4f713d8d9d4b5b1e3f","file_id":"6973","creator":"dernst","file_size":2243134}],"month":"04","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":1,"external_id":{"isi":["000491042100002"],"arxiv":["1901.06447"]},"page":"835-854","doi":"10.1007/s11263-019-01219-8","language":[{"iso":"eng"}],"article_type":"original","volume":128,"department":[{"_id":"ChLa"}],"type":"journal_article","scopus_import":"1","date_updated":"2026-07-28T13:01:49Z","author":[{"first_name":"Paul M","full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","last_name":"Henderson"},{"last_name":"Ferrari","full_name":"Ferrari, Vittorio","first_name":"Vittorio"}],"year":"2020","isi":1,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","publication":"International Journal of Computer Vision","date_published":"2020-04-01T00:00:00Z","OA_place":"publisher","has_accepted_license":"1","corr_author":"1","quality_controlled":"1","ddc":["004"],"abstract":[{"lang":"eng","text":"We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn."}],"publisher":"Springer Nature","intvolume":"       128"},{"_id":"6185","fulldoi":"https://doi.org/10.1007/s00220-019-03657-4","title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-11-18T11:14:37Z","citation":{"ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. <i>Communications in Mathematical Physics</i>. 2020;378:1203-1278. doi:<a href=\"https://doi.org/10.1007/s00220-019-03657-4\">10.1007/s00220-019-03657-4</a>","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03657-4\">https://doi.org/10.1007/s00220-019-03657-4</a>.","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.","apa":"Erdös, L., Krüger, T. H., &#38; Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03657-4\">https://doi.org/10.1007/s00220-019-03657-4</a>","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” <i>Communications in Mathematical Physics</i>, vol. 378. Springer Nature, pp. 1203–1278, 2020.","mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” <i>Communications in Mathematical Physics</i>, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:<a href=\"https://doi.org/10.1007/s00220-019-03657-4\">10.1007/s00220-019-03657-4</a>.","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278."},"ec_funded":1,"status":"public","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"date_created":"2019-03-28T10:21:15Z","file":[{"checksum":"c3a683e2afdcea27afa6880b01e53dc2","file_size":2904574,"creator":"dernst","success":1,"file_id":"8771","date_created":"2020-11-18T11:14:37Z","file_name":"2020_CommMathPhysics_Erdoes.pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-11-18T11:14:37Z","content_type":"application/pdf"}],"month":"09","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"page":"1203-1278","external_id":{"arxiv":["1809.03971"],"isi":["000529483000001"]},"language":[{"iso":"eng"}],"article_type":"original","doi":"10.1007/s00220-019-03657-4","related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"volume":378,"department":[{"_id":"LaEr"}],"scopus_import":"1","type":"journal_article","date_updated":"2026-07-29T13:46:19Z","author":[{"orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László"},{"first_name":"Torben H","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","last_name":"Krüger"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J"}],"year":"2020","isi":1,"arxiv":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","article_processing_charge":"Yes (via OA deal)","publication":"Communications in Mathematical Physics","date_published":"2020-09-01T00:00:00Z","has_accepted_license":"1","quality_controlled":"1","ddc":["530","510"],"abstract":[{"text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).","lang":"eng"}],"publisher":"Springer Nature","intvolume":"       378"}]