[{"status":"public","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","ddc":["580"],"intvolume":" 41","_id":"462","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2018_PlantCellEnv_Fan.pdf","creator":"dernst","content_type":"application/pdf","file_size":1937976,"file_id":"7042","relation":"main_file","checksum":"6a20f843565f962cb20281cdf5e40914","date_created":"2019-11-18T16:22:22Z","date_updated":"2020-07-14T12:46:32Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"article_type":"original","page":"850 - 864","publication":"Plant, Cell and Environment","citation":{"ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153."},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","year":"2018","pmid":1,"date_created":"2018-12-11T11:46:36Z","date_updated":"2023-09-13T09:03:18Z","volume":41,"author":[{"full_name":"Fan, Ligang","first_name":"Ligang","last_name":"Fan"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"first_name":"Wei","last_name":"Hu","full_name":"Hu, Wei"},{"last_name":"Li","first_name":"Weina","full_name":"Li, Weina"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"full_name":"Jiang, Liwen","first_name":"Liwen","last_name":"Jiang"},{"first_name":"Quan","last_name":"Qiu","full_name":"Qiu, Quan"}],"file_date_updated":"2020-07-14T12:46:32Z","publist_id":"7359","quality_controlled":"1","isi":1,"external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/pce.13153","month":"05"},{"year":"2018","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","department":[{"_id":"BjHo"}],"publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Altmeyer","first_name":"Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian"}],"volume":452,"date_created":"2018-12-11T11:46:56Z","date_updated":"2023-09-13T09:03:44Z","publist_id":"7297","file_date_updated":"2020-07-14T12:46:37Z","external_id":{"isi":["000425547700061"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.jmmm.2017.12.073","language":[{"iso":"eng"}],"month":"04","_id":"519","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 452","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","ddc":["530"],"status":"public","file":[{"relation":"main_file","file_id":"7838","date_updated":"2020-07-14T12:46:37Z","date_created":"2020-05-14T14:41:17Z","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_name":"2018_Magnetism_Altmeyer.pdf","access_level":"open_access","file_size":17309535,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ","lang":"eng"}],"citation":{"ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073."},"publication":"Journal of Magnetism and Magnetic Materials","page":"427 - 441","article_type":"original","date_published":"2018-04-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15"},{"page":"181-201","citation":{"ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11."},"date_published":"2018-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 11275","title":"New approaches for almost-sure termination of probabilistic programs","status":"public","_id":"5679","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}],"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000916310900011"],"arxiv":["1806.06683"]},"main_file_link":[{"url":"http://arxiv.org/abs/1806.06683","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-02768-1_11","conference":{"end_date":"2018-12-06","start_date":"2018-12-02","location":"Wellington, New Zealand","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"publication_identifier":{"issn":["03029743"],"isbn":["9783030027674"]},"month":"12","department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"full_name":"Ryu, Sukyoung","last_name":"Ryu","first_name":"Sukyoung"}],"year":"2018","volume":11275,"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-09-13T09:02:22Z","author":[{"full_name":"Huang, Mingzhang","first_name":"Mingzhang","last_name":"Huang"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2023-09-13T09:01:56Z","date_created":"2018-12-11T11:47:06Z","volume":48,"author":[{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"year":"2018","publist_id":"7268","language":[{"iso":"eng"}],"doi":"10.1016/j.conb.2017.12.005","isi":1,"quality_controlled":"1","external_id":{"isi":["000427101600018"]},"month":"02","oa_version":"None","title":"Neural stem cells in neuropsychiatric disorders","status":"public","intvolume":" 48","_id":"546","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}],"issue":"2","type":"journal_article","date_published":"2018-02-01T00:00:00Z","page":"131 - 138","publication":"Current Opinion in Neurobiology","citation":{"chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005"},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401414.v1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"citation":{"mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018."},"oa":1,"day":"31","month":"05","article_processing_charge":"No","date_created":"2021-08-06T12:58:25Z","date_updated":"2023-09-13T09:01:31Z","oa_version":"Published Version","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"full_name":"Schaefer, Martin","first_name":"Martin","last_name":"Schaefer"}],"related_material":{"record":[{"id":"279","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"_id":"9812","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"type":"research_data_reference"},{"oa_version":"Preprint","date_updated":"2023-09-13T09:01:31Z","date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"id":"279","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"last_name":"Pich","first_name":"Oriol","full_name":"Pich, Oriol"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","year":"2018","_id":"9811","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"type":"research_data_reference","date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1","oa":1,"citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"article_processing_charge":"No","day":"31","month":"05"},{"type":"journal_article","issue":"1","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"intvolume":" 19","status":"public","ddc":["570"],"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","_id":"20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":4629784,"content_type":"application/pdf","creator":"dernst","file_name":"2018_BMCGenomics_Higareda.pdf","access_level":"open_access","date_created":"2018-12-17T14:52:57Z","date_updated":"2020-07-14T12:45:23Z","checksum":"a56516e734dab589dc7f3e1915973b4d","relation":"main_file","file_id":"5712"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","article_type":"original","citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0."},"publication":"BMC Genomics","date_published":"2018-11-03T00:00:00Z","publist_id":"8035","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","publication_status":"published","year":"2018","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","volume":19,"date_updated":"2023-09-13T09:10:47Z","date_created":"2018-12-11T11:44:12Z","related_material":{"record":[{"id":"9807","relation":"research_data","status":"public"},{"id":"9808","status":"public","relation":"research_data"}]},"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"publication_identifier":{"issn":["1471-2164"]},"month":"11","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000450976700002"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5173-0"},{"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000442938200004"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3178432","month":"08","department":[{"_id":"KrPi"}],"publisher":"ACM","publication_status":"published","year":"2018","volume":65,"date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T09:05:17Z","author":[{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"article_number":"20","ec_funded":1,"publist_id":"7947","article_type":"original","citation":{"ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432."},"publication":"Journal of the ACM","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 65","title":"Non-malleable codes","status":"public","_id":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}]},{"title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","status":"public","intvolume":" 217","_id":"5676","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.","lang":"eng"}],"issue":"12","page":"4267-4283","publication":"Journal of Cell Biology","citation":{"ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048."},"date_published":"2018-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"CaHe"}],"year":"2018","pmid":1,"date_updated":"2023-09-13T09:11:17Z","date_created":"2018-12-16T22:59:19Z","volume":217,"author":[{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"last_name":"Patricio","first_name":"Pedro","full_name":"Patricio, Pedro"},{"first_name":"Susana","last_name":"Ponte","full_name":"Ponte, Susana"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Almeida, Luis","last_name":"Almeida","first_name":"Luis"},{"last_name":"Nunes","first_name":"André S.","full_name":"Nunes, André S."},{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"first_name":"Antonio","last_name":"Jacinto","full_name":"Jacinto, Antonio"}],"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"oa":1,"external_id":{"pmid":["30228162 "],"isi":["000451960800018"]},"language":[{"iso":"eng"}],"doi":"10.1083/jcb.201804048","month":"12","publication_identifier":{"issn":["00219525"]}},{"type":"research_data_reference","abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"publisher":"Springer Nature","department":[{"_id":"SiHi"}],"status":"public","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","_id":"9807","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","oa_version":"Published Version","date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:26:53Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20"}]},"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"full_name":"Giroud, Maude","last_name":"Giroud","first_name":"Maude"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","first_name":"Marcel","last_name":"Scheideler"}],"article_processing_charge":"No","month":"11","day":"03","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1"},"date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1"},{"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"related_material":{"record":[{"id":"20","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:31:57Z","oa_version":"Published Version","_id":"9808","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","status":"public","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","department":[{"_id":"SiHi"}],"publisher":"Springer Nature","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}],"type":"research_data_reference","doi":"10.6084/m9.figshare.7295369.v1","date_published":"2018-11-03T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295369.v1","open_access":"1"}],"citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1."},"oa":1,"month":"11","day":"03","article_processing_charge":"No"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","citation":{"ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534."},"page":"51 - 65","abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"type":"conference","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"193","title":"On the memory hardness of data independent password hashing functions","status":"public","month":"06","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","location":"Incheon, Republic of Korea","start_date":"2018-06-04","end_date":"2018-06-08"},"doi":"10.1145/3196494.3196534","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"oa":1,"external_id":{"isi":["000516620100005"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"ec_funded":1,"publist_id":"7723","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Reyzin, Lenoid","last_name":"Reyzin","first_name":"Lenoid"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal"}],"date_updated":"2023-09-13T09:13:12Z","date_created":"2018-12-11T11:45:07Z","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","year":"2018","publication_status":"published","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"publisher":"ACM"},{"month":"03","conference":{"end_date":"2018-05-03","start_date":"2018-04-29","location":"Tel Aviv, Israel","name":"Eurocrypt: Advances in Cryptology"},"doi":"10.1007/978-3-319-78381-9_1","language":[{"iso":"eng"}],"external_id":{"isi":["000517097500001"]},"main_file_link":[{"url":"https://eprint.iacr.org/2018/077","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"publist_id":"7581","ec_funded":1,"author":[{"last_name":"Micciancio","first_name":"Daniele","full_name":"Micciancio, Daniele"},{"last_name":"Walter","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"date_created":"2018-12-11T11:45:42Z","date_updated":"2023-09-13T09:12:04Z","volume":10820,"acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","year":"2018","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","day":"31","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-31T00:00:00Z","citation":{"ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1."},"page":"3 - 28","abstract":[{"text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","_id":"300","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"On the bit security of cryptographic primitives","intvolume":" 10820"},{"date_published":"2018-03-29T00:00:00Z","publication":"SIAM J Discrete Math","citation":{"ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.","short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782."},"article_type":"original","page":"750 - 782","day":"29","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","_id":"312","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the optimality of the FCC lattice for soft sphere packing","status":"public","intvolume":" 32","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"issue":"1","type":"journal_article","doi":"10.1137/16M1097201","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000428958900038"]},"main_file_link":[{"url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"month":"03","publication_identifier":{"issn":["08954801"]},"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-09-13T09:34:38Z","volume":32,"year":"2018","acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"HeEd"}],"publist_id":"7553"},{"external_id":{"arxiv":["1805.01652"],"isi":["000430402700009"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.crma.2018.03.005","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["1631073X"]},"year":"2018","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"}],"date_updated":"2023-09-13T09:34:12Z","date_created":"2018-12-11T11:46:19Z","volume":356,"publist_id":"7420","publication":"Comptes Rendus Mathematique","citation":{"short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414."},"article_type":"original","page":"412-414","date_published":"2018-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","_id":"409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the number of non-hexagons in a planar tiling","status":"public","intvolume":" 356","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons.","lang":"eng"}],"issue":"4"},{"author":[{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"link":[{"url":"http://doi.org/10.1038/s41562-018-0342-3","relation":"erratum"}]},"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-13T09:38:54Z","volume":2,"year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:46:25Z","ec_funded":1,"publist_id":"7404","doi":"10.1038/s41562-018-0320-9","language":[{"iso":"eng"}],"external_id":{"isi":["000446612000016"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"03","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:46:25Z","date_created":"2019-11-19T08:19:51Z","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb","file_id":"7052","relation":"main_file","creator":"dernst","file_size":598033,"content_type":"application/pdf","file_name":"2018_NatureHumanBeh_Hilbe.pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"419","status":"public","ddc":["000"],"title":"Partners and rivals in direct reciprocity","intvolume":" 2","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"type":"journal_article","date_published":"2018-03-19T00:00:00Z","publication":"Nature Human Behaviour","citation":{"chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9"},"article_type":"review","page":"469–477","day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated."}],"_id":"78","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Online timed pattern matching using automata","status":"public","intvolume":" 11022","file":[{"date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","checksum":"436b7574934324cfa7d1d3986fddc65b","file_id":"7831","relation":"main_file","creator":"dernst","file_size":374851,"content_type":"application/pdf","file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","citation":{"short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232."},"page":"215 - 232","date_published":"2018-08-26T00:00:00Z","file_date_updated":"2020-07-14T12:48:03Z","publist_id":"7976","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"full_name":"Asarin, Eugene","last_name":"Asarin","first_name":"Eugene"}],"date_created":"2018-12-11T11:44:31Z","date_updated":"2023-09-13T09:35:46Z","volume":11022,"month":"08","publication_identifier":{"isbn":["978-3-030-00150-6"]},"external_id":{"isi":["000884993200013"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"conference":{"end_date":"2018-09-06","start_date":"2018-09-04","location":"Bejing, China","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"doi":"10.1007/978-3-030-00151-3_13","language":[{"iso":"eng"}]},{"month":"04","doi":"10.1038/s41598-018-24004-y","language":[{"iso":"eng"}],"external_id":{"isi":["000429404300013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publist_id":"7548","file_date_updated":"2020-07-14T12:46:02Z","article_number":"5690","author":[{"full_name":"Brauns, Matthias","last_name":"Brauns","first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sergey","last_name":"Amitonov","full_name":"Amitonov, Sergey"},{"first_name":"Paul","last_name":"Spruijtenburg","full_name":"Spruijtenburg, Paul"},{"full_name":"Zwanenburg, Floris","first_name":"Floris","last_name":"Zwanenburg"}],"volume":8,"date_updated":"2023-09-13T09:38:00Z","date_created":"2018-12-11T11:45:47Z","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"GeKa"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","date_published":"2018-04-09T00:00:00Z","citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y"},"publication":"Scientific Reports","issue":"1","abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"type":"journal_article","pubrep_id":"1016","file":[{"date_updated":"2020-07-14T12:46:02Z","date_created":"2018-12-12T10:17:04Z","checksum":"20af238ca4ba6491b77270be8d826bf5","file_id":"5256","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1850530,"file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"317","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 8","status":"public","title":"Palladium gates for reproducible quantum dots in silicon","ddc":["539"]},{"oa":1,"external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1096/fj.201800443"}],"isi":1,"quality_controlled":"1","project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"doi":"10.1096/fj.201800443","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["08926638"]},"year":"2018","pmid":1,"publication_status":"published","publisher":"FASEB","department":[{"_id":"SyCr"}],"author":[{"full_name":"Liutkeviciute, Zita","first_name":"Zita","last_name":"Liutkeviciute"},{"full_name":"Gil Mansilla, Esther","first_name":"Esther","last_name":"Gil Mansilla"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Giulia Di Giglio","full_name":"Giulia Di Giglio, Maria"},{"first_name":"Edin","last_name":"Muratspahić","full_name":"Muratspahić, Edin"},{"last_name":"Grebien","first_name":"Florian","full_name":"Grebien, Florian"},{"first_name":"Thomas","last_name":"Rattei","full_name":"Rattei, Thomas"},{"full_name":"Muttenthaler, Markus","first_name":"Markus","last_name":"Muttenthaler"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"last_name":"Gruber","first_name":"Christian","full_name":"Gruber, Christian"}],"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-13T09:37:32Z","volume":32,"publist_id":"7721","publication":"The FASEB Journal","citation":{"ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443."},"article_type":"original","page":"6808-6821","date_published":"2018-11-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"194","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","status":"public","intvolume":" 32","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"issue":"12"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41589-018-0090-8","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000438970200010"]},"month":"07","volume":14,"date_created":"2018-12-11T11:44:56Z","date_updated":"2023-09-13T09:36:35Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"author":[{"first_name":"Timm","last_name":"Fehrentz","full_name":"Fehrentz, Timm"},{"full_name":"Huber, Florian","first_name":"Florian","last_name":"Huber"},{"full_name":"Hartrampf, Nina","last_name":"Hartrampf","first_name":"Nina"},{"full_name":"Bruegmann, Tobias","last_name":"Bruegmann","first_name":"Tobias"},{"last_name":"Frank","first_name":"James","full_name":"Frank, James"},{"full_name":"Fine, Nicholas","last_name":"Fine","first_name":"Nicholas"},{"first_name":"Daniela","last_name":"Malan","full_name":"Malan, Daniela"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"},{"first_name":"Denis","last_name":"Tikhonov","full_name":"Tikhonov, Denis"},{"first_name":"Maritn","last_name":"Sumser","full_name":"Sumser, Maritn"},{"last_name":"Sasse","first_name":"Philipp","full_name":"Sasse, Philipp"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"first_name":"Boris","last_name":"Zhorov","full_name":"Zhorov, Boris"},{"full_name":"Klocker, Nikolaj","first_name":"Nikolaj","last_name":"Klocker"},{"full_name":"Trauner, Dirk","first_name":"Dirk","last_name":"Trauner"}],"department":[{"_id":"JoDa"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2018","publist_id":"7762","file_date_updated":"2020-07-14T12:45:03Z","date_published":"2018-07-16T00:00:00Z","page":"764 - 767","article_type":"original","citation":{"ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8."},"publication":"Nature Chemical Biology","article_processing_charge":"No","has_accepted_license":"1","day":"16","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_id":"7832","relation":"main_file","date_updated":"2020-07-14T12:45:03Z","date_created":"2020-05-14T12:14:09Z","checksum":"d42935094ec845f54a0688bf12986d62","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","access_level":"open_access","creator":"dernst","file_size":6321000,"content_type":"application/pdf"}],"intvolume":" 14","ddc":["570"],"status":"public","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","_id":"159","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"8","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"type":"journal_article"},{"abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11024","title":"Parameter-independent strategies for pMDPs via POMDPs","status":"public","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-08-15T00:00:00Z","page":"53-70","citation":{"short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70."},"publist_id":"7975","volume":11024,"date_created":"2018-12-11T11:44:31Z","date_updated":"2023-09-13T09:38:28Z","author":[{"full_name":"Arming, Sebastian","last_name":"Arming","first_name":"Sebastian"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-99154-2_4","conference":{"start_date":"2018-09-04","location":"Beijing, China","end_date":"2018-09-07","name":"QEST: Quantitative Evaluation of Systems"},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1806.05126"],"isi":["000548912200004"]},"main_file_link":[{"url":"https://arxiv.org/abs/1806.05126","open_access":"1"}]},{"page":"1507 - 1527","publication":"Annales Henri Poincare","citation":{"mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018."},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","title":"Persistence of translational symmetry in the BCS model with radial pair interaction","status":"public","ddc":["510"],"intvolume":" 19","_id":"400","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":582680,"creator":"system","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:12:47Z","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","relation":"main_file","file_id":"4966"}],"pubrep_id":"1011","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case."}],"issue":"5","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429799900008"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0665-7","month":"05","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"year":"2018","date_created":"2018-12-11T11:46:15Z","date_updated":"2023-09-15T12:04:15Z","volume":19,"author":[{"full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746"},{"full_name":"Geisinge, Alissa","first_name":"Alissa","last_name":"Geisinge"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"first_name":"Michael","last_name":"Loss","full_name":"Loss, Michael"}],"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7429","ec_funded":1},{"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7423","author":[{"full_name":"Bod’Ová, Katarína","last_name":"Bod’Ová","first_name":"Katarína"},{"id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","first_name":"Gabriel","full_name":"Mitchell, Gabriel"},{"full_name":"Harpaz, Roy","first_name":"Roy","last_name":"Harpaz"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9831"}]},"date_updated":"2023-09-15T12:06:19Z","date_created":"2018-12-11T11:46:18Z","volume":13,"year":"2018","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"month":"03","doi":"10.1371/journal.pone.0193049","language":[{"iso":"eng"}],"external_id":{"isi":["000426896800032"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"issue":"3","type":"journal_article","pubrep_id":"995","file":[{"file_id":"5165","relation":"main_file","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z","checksum":"684229493db75b43e98a46cd922da497","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":6887358}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"406","ddc":["530","571"],"title":"Probabilistic models of individual and collective animal behavior","status":"public","intvolume":" 13","day":"07","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2018-03-07T00:00:00Z","publication":"PLoS One","citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049"}},{"page":"359 - 366","publication":"Nature Ecology and Evolution","citation":{"mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z.","ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018."},"date_published":"2018-02-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","intvolume":" 2","_id":"457","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","abstract":[{"text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages","lang":"eng"}],"issue":"2","quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"external_id":{"isi":["000426516400027"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41559-017-0424-z","month":"02","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2018","date_updated":"2023-09-15T12:04:57Z","date_created":"2018-12-11T11:46:35Z","volume":2,"author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz"},{"full_name":"Refardt, Dominik","first_name":"Dominik","last_name":"Refardt"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"publist_id":"7364","ec_funded":1},{"doi":"10.1016/j.cub.2018.08.063","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"external_id":{"isi":["000446693400008"]},"quality_controlled":"1","isi":1,"month":"10","author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"},{"full_name":"Metzler, Sina","first_name":"Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494"},{"first_name":"Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"volume":28,"date_updated":"2023-09-15T12:06:46Z","date_created":"2018-12-11T11:44:23Z","year":"2018","department":[{"_id":"SyCr"}],"publisher":"Cell Press","publication_status":"published","publist_id":"7999","date_published":"2018-10-08T00:00:00Z","citation":{"ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063."},"publication":"Current Biology","page":"R1139 - R1140","article_type":"original","article_processing_charge":"No","day":"08","scopus_import":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"55","intvolume":" 28","status":"public","title":"Protection against the lethal side effects of social immunity in ants","issue":"19","abstract":[{"lang":"eng","text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation."}],"type":"journal_article"},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"3271 - 3290","citation":{"chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125"},"publication":"SIAM Journal on Mathematical Analysis","date_published":"2018-01-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.","lang":"eng"}],"intvolume":" 50","status":"public","title":"Power law decay for systems of randomly coupled differential equations","_id":"181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"01","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"258F40A4-B435-11E9-9278-68D0E5697425","grant_number":"M02080","call_identifier":"FWF","name":"Structured Non-Hermitian Random Matrices"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"external_id":{"isi":["000437018500032"],"arxiv":["1708.01546"]},"language":[{"iso":"eng"}],"doi":"10.1137/17M1143125","publist_id":"7740","ec_funded":1,"publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2018","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","volume":50,"date_created":"2018-12-11T11:45:03Z","date_updated":"2023-09-15T12:05:52Z","author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"first_name":"David T","last_name":"Renfrew","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3493-121X","full_name":"Renfrew, David T"}]},{"abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 506","status":"public","title":"Quantizations of multiplicative hypertoric varieties at a root of unity","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"322","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2018-07-15T00:00:00Z","page":"92 - 128","citation":{"short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015.","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128."},"publication":"Journal of Algebra","publist_id":"7543","ec_funded":1,"volume":506,"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-15T12:08:38Z","author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","last_name":"Ganev","first_name":"Iordan V","full_name":"Ganev, Iordan V"}],"department":[{"_id":"TaHa"}],"publisher":"World Scientific Publishing","publication_status":"published","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.jalgebra.2018.03.015","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.7211"}],"oa":1},{"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"title":"Implementation of the inference method in Matlab","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9831","year":"2018","oa_version":"Published Version","date_updated":"2023-09-15T12:06:18Z","date_created":"2021-08-09T07:01:24Z","related_material":{"record":[{"id":"406","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Bod’Ová, Katarína","first_name":"Katarína","last_name":"Bod’Ová"},{"full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Mitchell"},{"last_name":"Harpaz","first_name":"Roy","full_name":"Harpaz, Roy"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish."}],"citation":{"chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","mla":"Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001"},"doi":"10.1371/journal.pone.0193049.s001","date_published":"2018-03-07T00:00:00Z","article_processing_charge":"No","month":"03","day":"07"},{"intvolume":" 10981","ddc":["000"],"status":"public","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"142","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-17T15:57:06Z","checksum":"fd95e8026deacef3dc752a733bb9355f","relation":"main_file","file_id":"5718","file_size":5591566,"content_type":"application/pdf","creator":"dernst","file_name":"2018_LNCS_Kong.pdf","access_level":"open_access"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"page":"449 - 467","citation":{"ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24."},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","year":"2018","volume":10981,"date_updated":"2023-09-15T12:12:08Z","date_created":"2018-12-11T11:44:51Z","author":[{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"publist_id":"7781","file_date_updated":"2020-07-14T12:44:53Z","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000491481600024"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_24","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"month":"07"},{"month":"02","doi":"10.1103/PhysRevA.97.022510","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.07920","open_access":"1"}],"external_id":{"arxiv":["1802.07920"],"isi":["000425601000004"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"isi":1,"quality_controlled":"1","ec_funded":1,"publist_id":"7396","article_number":"022510","author":[{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Loureiro, Ulisses","first_name":"Ulisses","last_name":"Loureiro"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"first_name":"Paul","last_name":"Indelicato","full_name":"Indelicato, Paul"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"last_name":"Santos","first_name":"José","full_name":"Santos, José"}],"volume":97,"date_updated":"2023-09-15T12:09:35Z","date_created":"2018-12-11T11:46:25Z","year":"2018","acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","article_processing_charge":"No","day":"21","scopus_import":"1","date_published":"2018-02-21T00:00:00Z","citation":{"chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.","short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.","ieee":"P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018.","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510"},"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","article_type":"original","issue":"2","abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"427","intvolume":" 97","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","status":"public"},{"month":"01","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2018-01-10","start_date":"2018-01-07","location":"New Orleans, LA, USA"},"doi":"10.1137/1.9781611975031.20","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"external_id":{"isi":["000483921200021"],"arxiv":["1709.09209"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"publist_id":"7556","author":[{"full_name":"Akitaya, Hugo","first_name":"Hugo","last_name":"Akitaya"},{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"last_name":"Tóth","first_name":"Csaba","full_name":"Tóth, Csaba"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"6982"}]},"date_updated":"2023-09-15T12:19:32Z","date_created":"2018-12-11T11:45:45Z","year":"2018","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","citation":{"chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.","mla":"Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20.","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20"},"page":"274 - 292","abstract":[{"text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"309","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Recognizing weak embeddings of graphs","status":"public"},{"doi":"10.1103/PhysRevLett.121.255302","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"external_id":{"isi":["000454178600009"],"arxiv":["1809.00222"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"}],"month":"12","publication_identifier":{"issn":["00319007"]},"author":[{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp","last_name":"Yakaboylu"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","first_name":"Mikhail"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"date_updated":"2023-09-15T12:09:06Z","date_created":"2019-01-06T22:59:12Z","volume":121,"year":"2018","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"ec_funded":1,"article_number":"255302","date_published":"2018-12-17T00:00:00Z","publication":"Physical Review Letters","citation":{"ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018.","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302.","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302."},"article_type":"original","day":"17","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"5794","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Quantum groups as hidden symmetries of quantum impurities","intvolume":" 121","abstract":[{"text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems.","lang":"eng"}],"issue":"25","type":"journal_article"},{"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics."}],"intvolume":" 28","status":"public","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"3215 - 3238","article_type":"original","citation":{"ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389."},"publication":"Annals of Applied Probability","date_published":"2018-10-01T00:00:00Z","publist_id":"7967","publisher":"Institute of Mathematical Statistics","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2018","volume":28,"date_created":"2018-12-11T11:44:33Z","date_updated":"2023-09-15T12:10:35Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6287"}]},"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","last_name":"Nikitenko","first_name":"Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"}],"month":"10","project":[{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"oa":1,"external_id":{"isi":["000442893500018"],"arxiv":["1705.02870"]},"language":[{"iso":"eng"}],"doi":"10.1214/18-AAP1389"},{"author":[{"last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas"},{"full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc"},{"full_name":"Hagihara, Shinya","last_name":"Hagihara","first_name":"Shinya"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"last_name":"Uchida","first_name":"Naoyuki","full_name":"Uchida, Naoyuki"},{"first_name":"Keiko U","last_name":"Torii","full_name":"Torii, Keiko U"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-15T12:11:03Z","volume":4,"year":"2018","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publist_id":"7728","doi":"10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"external_id":{"pmid":["29942048"],"isi":["000443221200017"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"06","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"192","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","status":"public","intvolume":" 4","abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2018-06-25T00:00:00Z","publication":"Nature Plants","citation":{"short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459."},"article_type":"original","page":"453 - 459","day":"25","article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566."},"date_published":"2018-11-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"issue":"11","status":"public","ddc":["580"],"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","intvolume":" 19","_id":"14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_created":"2018-12-17T16:04:11Z","date_updated":"2020-07-14T12:44:50Z","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","file_id":"5719","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2200593,"file_name":"2018_IJMS_Hille.pdf","access_level":"open_access"}],"month":"11","publication_identifier":{"eissn":["1422-0067"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"external_id":{"isi":["000451528500282"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/ijms19113566","file_date_updated":"2020-07-14T12:44:50Z","publist_id":"8042","ec_funded":1,"publication_status":"published","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"publisher":"MDPI","year":"2018","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-18T08:09:32Z","volume":19,"author":[{"first_name":"Sander","last_name":"Hille","full_name":"Hille, Sander"},{"full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}]},{"type":"journal_article","issue":"4","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"intvolume":" 210","status":"public","title":"Replicability of introgression under linked, polygenic selection","_id":"39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"04","page":"1411-1427","article_type":"original","citation":{"ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429."},"publication":"Genetics","date_published":"2018-12-04T00:00:00Z","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2018","volume":210,"date_updated":"2023-09-18T08:10:29Z","date_created":"2018-12-11T11:44:18Z","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["00166731"]},"month":"12","quality_controlled":"1","isi":1,"external_id":{"isi":["000452315900021"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429"},{"date_published":"2018-07-10T00:00:00Z","publication":"International Journal of Modern Physics B","citation":{"ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022."},"page":"1840022","day":"10","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"420","status":"public","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","intvolume":" 32","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"issue":"17","type":"journal_article","doi":"10.1142/S0217979218400222","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"external_id":{"isi":["000438217300007"]},"oa":1,"quality_controlled":"1","isi":1,"month":"07","author":[{"first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Luca","last_name":"Salasnich","full_name":"Salasnich, Luca"}],"date_updated":"2023-09-18T08:09:59Z","date_created":"2018-12-11T11:46:22Z","volume":32,"year":"2018","publication_status":"published","publisher":"World Scientific Publishing","department":[{"_id":"MiLe"}],"publist_id":"7402"},{"status":"public","ddc":["570"],"title":"Selection and gene flow shape genomic islands that control floral guides","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","oa_version":"Published Version","file":[{"file_id":"5683","relation":"main_file","date_created":"2018-12-17T08:44:03Z","date_updated":"2020-07-14T12:46:16Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","file_name":"11006.full.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1911302}],"type":"journal_article","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"issue":"43","page":"11006 - 11011","publication":"PNAS","citation":{"chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"},"date_published":"2018-10-23T00:00:00Z","scopus_import":"1","day":"23","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","pmid":1,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","volume":115,"author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"full_name":"Whitley, Annabel","last_name":"Whitley","first_name":"Annabel"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"last_name":"Bradley","first_name":"Desmond","full_name":"Bradley, Desmond"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Elleouet, Joane","first_name":"Joane","last_name":"Elleouet"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"full_name":"Andalo, Christophe","first_name":"Christophe","last_name":"Andalo"},{"full_name":"Li, Miaomiao","last_name":"Li","first_name":"Miaomiao"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"full_name":"Rebocho, Alexandra B","first_name":"Alexandra B","last_name":"Rebocho"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","isi":1,"quality_controlled":"1","external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","month":"10","publication_identifier":{"issn":["00278424"]}},{"month":"05","doi":"10.1117/12.2309928","conference":{"name":"SPIE: The international society for optical engineering","end_date":"2018-04-26","start_date":"2018-04-22","location":"Strasbourg, France"},"language":[{"iso":"eng"}],"external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"isi":1,"quality_controlled":"1","publist_id":"7766","article_number":"106721N","author":[{"first_name":"André","last_name":"Xuereb","full_name":"Xuereb, André"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"}],"volume":10672,"date_updated":"2023-09-18T08:12:24Z","date_created":"2018-12-11T11:44:55Z","year":"2018","publisher":"SPIE","editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"full_name":"Nunzi, J M","first_name":"J M","last_name":"Nunzi"}],"department":[{"_id":"JoFi"}],"publication_status":"published","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-05-04T00:00:00Z","citation":{"chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928"},"abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"type":"conference","alternative_title":["Proceedings of SPIE"],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"155","intvolume":" 10672","title":"Routing thermal noise through quantum networks","status":"public"},{"issue":"6420","abstract":[{"lang":"eng","text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. "}],"type":"journal_article","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5767","intvolume":" 362","status":"public","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2018-12-14T00:00:00Z","citation":{"chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980"},"publication":"Science","page":"1271-1275","article_type":"original","author":[{"full_name":"Gotlieb, Kenneth","last_name":"Gotlieb","first_name":"Kenneth"},{"full_name":"Lin, Chiu-Yun","first_name":"Chiu-Yun","last_name":"Lin"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Wentao","last_name":"Zhang","full_name":"Zhang, Wentao"},{"first_name":"Christopher L.","last_name":"Smallwood","full_name":"Smallwood, Christopher L."},{"full_name":"Jozwiak, Christopher","last_name":"Jozwiak","first_name":"Christopher"},{"full_name":"Eisaki, Hiroshi","first_name":"Hiroshi","last_name":"Eisaki"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"full_name":"Vishwanath, Ashvin","first_name":"Ashvin","last_name":"Vishwanath"},{"first_name":"Alessandra","last_name":"Lanzara","full_name":"Lanzara, Alessandra"}],"volume":362,"date_updated":"2023-09-18T08:11:56Z","date_created":"2018-12-19T14:53:50Z","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","year":"2018","publisher":"American Association for the Advancement of Science","department":[{"_id":"MaSe"}],"publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"12","doi":"10.1126/science.aao0980","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000452994400048"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aao0980"}],"quality_controlled":"1","isi":1},{"publist_id":"7389","related_material":{"record":[{"id":"1205","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"full_name":"Liu, Han","last_name":"Liu","first_name":"Han"},{"first_name":"Huobing","last_name":"Song","full_name":"Song, Huobing"},{"last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui"},{"full_name":"Wang, Rui","last_name":"Wang","first_name":"Rui"},{"full_name":"Guan, Yong","first_name":"Yong","last_name":"Guan"},{"full_name":"Sha, Lui","last_name":"Sha","first_name":"Lui"}],"volume":19,"date_created":"2018-12-11T11:46:27Z","date_updated":"2023-09-18T08:12:49Z","year":"2018","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","month":"01","doi":"10.1109/TITS.2017.2778077","language":[{"iso":"eng"}],"external_id":{"isi":["000446651100020"]},"quality_controlled":"1","isi":1,"issue":"10","abstract":[{"lang":"eng","text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network."}],"type":"journal_article","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"434","intvolume":" 19","title":"Safety-assured model-driven design of the multifunction vehicle bus controller","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","citation":{"mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077.","ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077"},"publication":"IEEE Transactions on Intelligent Transportation Systems","page":"3320 - 3333"},{"month":"06","doi":"10.7554/eLife.34465","language":[{"iso":"eng"}],"external_id":{"isi":["000436227500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"publist_id":"7759","article_number":"e34465","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","first_name":"Julian","last_name":"Petersen"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"full_name":"Szarowska, Bara","last_name":"Szarowska","first_name":"Bara"},{"full_name":"Kastriti, Maria","last_name":"Kastriti","first_name":"Maria"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"last_name":"Spitz","first_name":"Francois","full_name":"Spitz, Francois"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"last_name":"Hovorakova","first_name":"Maria","full_name":"Hovorakova, Maria"},{"last_name":"Zikmund","first_name":"Tomas","full_name":"Zikmund, Tomas"},{"first_name":"Kazunori","last_name":"Sunadome","full_name":"Sunadome, Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"full_name":"Marklund, Ulrika","last_name":"Marklund","first_name":"Ulrika"},{"full_name":"Abdo, Hind","first_name":"Hind","last_name":"Abdo"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","first_name":"Pascal","last_name":"Maire"},{"full_name":"Wurmser, Maud","first_name":"Maud","last_name":"Wurmser"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"full_name":"Fried, Kaj","last_name":"Fried","first_name":"Kaj"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9838"}]},"date_updated":"2023-09-18T09:29:07Z","date_created":"2018-12-11T11:44:57Z","volume":7,"year":"2018","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"eLife Sciences Publications","day":"13","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-06-13T00:00:00Z","publication":"eLife","citation":{"apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465."},"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":9816484,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Kaucka.pdf","checksum":"da2378cdcf6b5461dcde194e4d608343","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-17T16:41:58Z","relation":"main_file","file_id":"5727"}],"_id":"162","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","ddc":["571"],"status":"public","intvolume":" 7"},{"page":"451 - 467","citation":{"mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15.","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15.","ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15"},"date_published":"2018-05-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"29","intvolume":" 10821","title":"Simple proofs of sequential work","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"302","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains.","lang":"eng"}],"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000517098700015"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/183.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-78375-8_15","conference":{"end_date":"2018-05-03","start_date":"2018-04-29","location":"Tel Aviv, Israel","name":"Eurocrypt: Advances in Cryptology"},"month":"05","department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":10821,"date_updated":"2023-09-18T09:29:33Z","date_created":"2018-12-11T11:45:42Z","author":[{"full_name":"Cohen, Bram","last_name":"Cohen","first_name":"Bram"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publist_id":"7579","ec_funded":1},{"month":"10","publication_identifier":{"issn":["24700045"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"external_id":{"isi":["000447486100004"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"doi":"10.1103/PhysRevE.98.042410","language":[{"iso":"eng"}],"article_number":"042410","ec_funded":1,"publist_id":"8024","year":"2018","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"author":[{"full_name":"Ferrari, Ulisse","last_name":"Ferrari","first_name":"Ulisse"},{"full_name":"Deny, Stephane","first_name":"Stephane","last_name":"Deny"},{"last_name":"Chalk","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-18T09:18:44Z","volume":98,"scopus_import":"1","day":"17","article_processing_charge":"No","publication":"Physical Review E","citation":{"chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.","mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410"},"article_type":"original","date_published":"2018-10-17T00:00:00Z","type":"journal_article","abstract":[{"text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.","lang":"eng"}],"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"31","title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","status":"public","intvolume":" 98","oa_version":"Preprint"},{"author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"last_name":"Guzmán Sáenz","first_name":"Aldo","full_name":"Guzmán Sáenz, Aldo"},{"full_name":"Prieto, Y","last_name":"Prieto","first_name":"Y"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","first_name":"Mikhail"},{"last_name":"Kalinina","first_name":"V","full_name":"Kalinina, V"},{"full_name":"Lupercio, Ernesto","first_name":"Ernesto","last_name":"Lupercio"}],"volume":115,"date_updated":"2023-09-18T08:41:16Z","date_created":"2018-12-11T11:44:26Z","year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"TaHa"}],"publication_status":"published","ec_funded":1,"publist_id":"7990","doi":"10.1073/pnas.1805847115","language":[{"iso":"eng"}],"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00278424"]},"month":"08","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"64","intvolume":" 115","status":"public","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","issue":"35","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"type":"journal_article","date_published":"2018-08-28T00:00:00Z","citation":{"ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115."},"publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","page":"E8135 - E8142","article_type":"original","article_processing_charge":"No","day":"28","scopus_import":"1"},{"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-09-18T09:29:07Z","date_created":"2021-08-09T12:54:35Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"162"}]},"author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria Eleni","last_name":"Kastriti","first_name":"Maria Eleni"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"last_name":"Annusver","first_name":"Karl","full_name":"Annusver, Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"full_name":"Symmons, Orsolya","first_name":"Orsolya","last_name":"Symmons"},{"first_name":"Leslie","last_name":"Pan","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"full_name":"Kaiser, Jozef","first_name":"Jozef","last_name":"Kaiser"},{"last_name":"Hovorakova","first_name":"Maria","full_name":"Hovorakova, Maria"},{"first_name":"Tomas","last_name":"Zikmund","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","first_name":"Kazunori","last_name":"Sunadome"},{"full_name":"Matise, Michael P","first_name":"Michael P","last_name":"Matise"},{"full_name":"Wang, Hui","first_name":"Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"first_name":"Patrik","last_name":"Ernfors","full_name":"Ernfors, Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"full_name":"Wurmser, Maud","last_name":"Wurmser","first_name":"Maud"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"last_name":"Fried","first_name":"Kaj","full_name":"Fried, Kaj"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"}],"department":[{"_id":"AnKi"}],"publisher":"Dryad","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","status":"public","_id":"9838","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","month":"06","day":"14","date_published":"2018-06-14T00:00:00Z","doi":"10.5061/dryad.f1s76f2","citation":{"ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2.","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.","mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"oa":1},{"publication":"Frontiers in Cellular Neuroscience","citation":{"ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311.","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311."},"article_type":"original","date_published":"2018-09-19T00:00:00Z","scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","_id":"41","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","status":"public","ddc":["570"],"intvolume":" 12","oa_version":"Published Version","file":[{"file_name":"fncel-12-00311.pdf","access_level":"open_access","creator":"dernst","file_size":6834251,"content_type":"application/pdf","file_id":"5684","relation":"main_file","date_created":"2018-12-17T08:49:03Z","date_updated":"2020-07-14T12:46:23Z","checksum":"0bcaec8d596162af0b7fe3f31325d480"}],"type":"journal_article","abstract":[{"text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.","lang":"eng"}],"external_id":{"isi":["000445090100002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"doi":"10.3389/fncel.2018.00311","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["16625102"]},"year":"2018","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Frontiers Media","author":[{"last_name":"Luján","first_name":"Rafæl","full_name":"Luján, Rafæl"},{"last_name":"Aguado","first_name":"Carolina","full_name":"Aguado, Carolina"},{"full_name":"Ciruela, Francisco","last_name":"Ciruela","first_name":"Francisco"},{"full_name":"Arus, Xavier","first_name":"Xavier","last_name":"Arus"},{"full_name":"Martín Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín Belmonte"},{"first_name":"Rocío","last_name":"Alfaro Ruiz","full_name":"Alfaro Ruiz, Rocío"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"last_name":"De La Ossa","first_name":"Luis","full_name":"De La Ossa, Luis"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Adelman, John","first_name":"John","last_name":"Adelman"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"}],"date_created":"2018-12-11T11:44:19Z","date_updated":"2023-09-18T09:31:18Z","volume":12,"article_number":"311","file_date_updated":"2020-07-14T12:46:23Z","publist_id":"8013","ec_funded":1},{"pubrep_id":"1065","file":[{"content_type":"application/pdf","file_size":1361441,"creator":"system","access_level":"open_access","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","checksum":"3e6034a94c6b5335e939145d88bdb371","date_created":"2018-12-12T10:16:08Z","date_updated":"2020-07-14T12:45:37Z","relation":"main_file","file_id":"5194"}],"oa_version":"Published Version","_id":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["530"],"title":"Single-shot readout of hole spins in Ge","status":"public","intvolume":" 18","abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2018-10-25T00:00:00Z","publication":"Nano Letters","citation":{"short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145."},"page":"7141 - 7145","day":"25","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"full_name":"Vukušić, Lada","first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"full_name":"Milem, Joshua M","first_name":"Joshua M","last_name":"Milem","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Friedrich","last_name":"Schäffler","full_name":"Schäffler, Friedrich"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"relation":"dissertation_contains","status":"public","id":"69"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"date_updated":"2023-09-18T09:30:37Z","date_created":"2018-12-11T11:44:13Z","volume":18,"year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"American Chemical Society","file_date_updated":"2020-07-14T12:45:37Z","publist_id":"8032","ec_funded":1,"doi":"10.1021/acs.nanolett.8b03217","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"}],"month":"10","publication_identifier":{"issn":["15306984"]}},{"oa":1,"external_id":{"isi":["000851042300031"]},"isi":1,"quality_controlled":"1","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"Euro-Par: European Conference on Parallel Processing","start_date":"2018-08-27","location":"Turin, Italy","end_date":"2018-08-31"},"doi":"10.1007/978-3-319-96983-1_33","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["03029743"]},"year":"2018","acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","publication_status":"published","publisher":"Springer","department":[{"_id":"DaAl"}],"author":[{"first_name":"Eran","last_name":"Gilad","full_name":"Gilad, Eran"},{"full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Oskin, Mark","first_name":"Mark","last_name":"Oskin"},{"full_name":"Etsion, Yoav","last_name":"Etsion","first_name":"Yoav"}],"date_updated":"2023-09-18T09:32:36Z","date_created":"2018-12-11T11:44:33Z","volume":11014,"file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7969","citation":{"ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479."},"page":"465 - 479","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","_id":"85","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","intvolume":" 11014","oa_version":"Preprint","file":[{"file_id":"5954","relation":"main_file","checksum":"13a3f250be8878405e791b53c19722ad","date_created":"2019-02-12T07:40:40Z","date_updated":"2020-07-14T12:48:14Z","access_level":"open_access","file_name":"2018_Brown.pdf","creator":"dernst","file_size":665372,"content_type":"application/pdf"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use.","lang":"eng"}]},{"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","year":"2018","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","date_created":"2018-12-11T11:45:50Z","date_updated":"2023-09-18T09:31:46Z","volume":97,"author":[{"last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"full_name":"Žnidarič, Marko","first_name":"Marko","last_name":"Žnidarič"},{"last_name":"Medvedyeva","first_name":"Mariya","full_name":"Medvedyeva, Mariya"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry"},{"full_name":"Prosen, Tomaž","last_name":"Prosen","first_name":"Tomaž"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"article_number":"104307","publist_id":"7538","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1706.05026","open_access":"1"}],"external_id":{"isi":["000427798800005"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.97.104307","month":"03","status":"public","title":"Slow dynamics in translation-invariant quantum lattice models","intvolume":" 97","_id":"327","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"issue":"10","publication":"Physical Review B","citation":{"ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307."},"date_published":"2018-03-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No"}]