[{"corr_author":"1","quality_controlled":"1","year":"2018","date_created":"2018-12-11T11:46:35Z","issue":"2","doi":"10.1038/s41559-017-0424-z","publication":"Nature Ecology and Evolution","page":"359 - 366","article_processing_charge":"No","abstract":[{"lang":"eng","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"}],"publication_status":"published","external_id":{"isi":["000426516400027"]},"title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Refardt, Dominik","last_name":"Refardt","first_name":"Dominik"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"},{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"volume":2,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"citation":{"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.","ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. 2018;2(2):359-366. doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>","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,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0424-z\">10.1038/s41559-017-0424-z</a>.","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.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., &#38; Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0424-z\">https://doi.org/10.1038/s41559-017-0424-z</a>"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","day":"01","isi":1,"language":[{"iso":"eng"}],"month":"02","date_published":"2018-02-01T00:00:00Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Springer Nature","date_updated":"2026-04-08T14:19:43Z","intvolume":"         2","oa_version":"None","type":"journal_article","publist_id":"7364","_id":"457","scopus_import":"1"},{"volume":370,"author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Bobenko, Alexander","first_name":"Alexander","last_name":"Bobenko"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Incircular nets and confocal conics","external_id":{"arxiv":["1602.04637"],"isi":["000423197800019"]},"publication_status":"published","abstract":[{"text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem.","lang":"eng"}],"article_processing_charge":"No","page":"2825 - 2854","publication":"Transactions of the American Mathematical Society","doi":"10.1090/tran/7292","issue":"4","date_created":"2018-12-11T11:46:35Z","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1602.04637","open_access":"1"}],"quality_controlled":"1","corr_author":"1","scopus_import":"1","_id":"458","publist_id":"7363","type":"journal_article","acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","intvolume":"       370","oa_version":"Preprint","date_updated":"2025-06-04T08:06:10Z","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society","arxiv":1,"date_published":"2018-04-01T00:00:00Z","month":"04","language":[{"iso":"eng"}],"oa":1,"isi":1,"day":"01","status":"public","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"citation":{"ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” <i>Transactions of the American Mathematical Society</i>, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. <i>Transactions of the American Mathematical Society</i>. 2018;370(4):2825-2854. doi:<a href=\"https://doi.org/10.1090/tran/7292\">10.1090/tran/7292</a>","apa":"Akopyan, A., &#38; Bobenko, A. (2018). Incircular nets and confocal conics. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7292\">https://doi.org/10.1090/tran/7292</a>","chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2018. <a href=\"https://doi.org/10.1090/tran/7292\">https://doi.org/10.1090/tran/7292</a>.","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” <i>Transactions of the American Mathematical Society</i>, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:<a href=\"https://doi.org/10.1090/tran/7292\">10.1090/tran/7292</a>."}},{"article_number":"161122","date_created":"2018-12-11T11:44:20Z","year":"2018","publication":"Physical Review B","doi":"10.1103/PhysRevB.98.161122","issue":"16","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.08316"}],"volume":98,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"first_name":"Norman","last_name":"Yao","full_name":"Yao, Norman"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Pollmann, Frank","first_name":"Frank","last_name":"Pollmann"},{"last_name":"Trauzettel","first_name":"Björn","full_name":"Trauzettel, Björn"}],"external_id":{"arxiv":["1806.08316"],"isi":["000448596500002"]},"publication_status":"published","abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"article_processing_charge":"No","title":"Detection and characterization of many-body localization in central spin models","day":"15","status":"public","citation":{"ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. 2018;98(16). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” <i>Physical Review B</i>, vol. 98, no. 16. American Physical Society, 2018.","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>.","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., &#38; Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>."},"type":"journal_article","acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","intvolume":"        98","oa_version":"Preprint","article_type":"original","scopus_import":"1","_id":"46","publist_id":"8008","oa":1,"isi":1,"date_updated":"2023-09-11T12:55:03Z","publisher":"American Physical Society","arxiv":1,"department":[{"_id":"MaSe"}],"date_published":"2018-10-15T00:00:00Z","month":"10","language":[{"iso":"eng"}]},{"year":"2018","date_created":"2018-12-11T11:46:36Z","doi":"10.1111/pce.13153","publication":"Plant, Cell and Environment","file":[{"file_id":"7042","access_level":"open_access","relation":"main_file","checksum":"6a20f843565f962cb20281cdf5e40914","file_size":1937976,"date_updated":"2020-07-14T12:46:32Z","date_created":"2019-11-18T16:22:22Z","file_name":"2018_PlantCellEnv_Fan.pdf","content_type":"application/pdf","creator":"dernst"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["580"],"author":[{"full_name":"Fan, Ligang","last_name":"Fan","first_name":"Ligang"},{"full_name":"Zhao, Lei","first_name":"Lei","last_name":"Zhao"},{"full_name":"Hu, Wei","last_name":"Hu","first_name":"Wei"},{"first_name":"Weina","last_name":"Li","full_name":"Li, Weina"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Shen, Jinbo","first_name":"Jinbo","last_name":"Shen"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"full_name":"Qiu, Quan","last_name":"Qiu","first_name":"Quan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":41,"pmid":1,"page":"850 - 864","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"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. ","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"day":"01","status":"public","citation":{"ieee":"L. Fan <i>et al.</i>, “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” <i>Plant, Cell and Environment</i>, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","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.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. <i>Plant, Cell and Environment</i>. 2018;41:850-864. doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>","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.","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. <i>Plant, Cell and Environment</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>","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.” <i>Plant, Cell and Environment</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” <i>Plant, Cell and Environment</i>, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>."},"article_type":"original","oa_version":"Submitted Version","intvolume":"        41","type":"journal_article","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. ","publist_id":"7359","_id":"462","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:46:32Z","month":"05","language":[{"iso":"eng"}],"date_published":"2018-05-01T00:00:00Z","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","date_updated":"2023-09-13T09:03:18Z"},{"quality_controlled":"1","corr_author":"1","year":"2018","date_created":"2018-12-11T11:46:50Z","publication":"Journal of Biotechnology","doi":"10.1016/j.jbiotec.2018.01.008","abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"external_id":{"isi":["000425715100006"]},"publication_status":"published","page":"40 - 52","article_processing_charge":"No","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","volume":268,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek","first_name":"Kathrin"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"acknowledged_ssus":[{"_id":"Bio"}],"citation":{"ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>.","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>."},"status":"public","day":"20","isi":1,"publisher":"Elsevier","department":[{"_id":"CaGu"}],"date_updated":"2024-10-09T20:58:29Z","month":"02","language":[{"iso":"eng"}],"date_published":"2018-02-20T00:00:00Z","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","type":"journal_article","intvolume":"       268","oa_version":"None","_id":"503","scopus_import":"1","publist_id":"7317"},{"date_created":"2018-12-11T11:46:56Z","year":"2018","publication":"Journal of Magnetism and Magnetic Materials","doi":"10.1016/j.jmmm.2017.12.073","quality_controlled":"1","file":[{"file_name":"2018_Magnetism_Altmeyer.pdf","content_type":"application/pdf","date_created":"2020-05-14T14:41:17Z","creator":"dernst","file_id":"7838","file_size":17309535,"date_updated":"2020-07-14T12:46:37Z","relation":"main_file","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","access_level":"open_access"}],"corr_author":"1","ddc":["530"],"has_accepted_license":"1","volume":452,"author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","first_name":"Sebastian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000425547700061"]},"publication_status":"published","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"}],"article_processing_charge":"No","page":"427 - 441","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","status":"public","day":"15","citation":{"ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. 2018;452:427-441. doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>","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.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452. Elsevier, pp. 427–441, 2018.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452, Elsevier, 2018, pp. 427–41, doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>.","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>"},"type":"journal_article","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","oa_version":"Submitted Version","intvolume":"       452","article_type":"original","scopus_import":"1","_id":"519","publist_id":"7297","file_date_updated":"2020-07-14T12:46:37Z","oa":1,"isi":1,"date_updated":"2024-10-09T20:58:32Z","department":[{"_id":"BjHo"}],"publisher":"Elsevier","date_published":"2018-04-15T00:00:00Z","month":"04","language":[{"iso":"eng"}]},{"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems"}],"citation":{"apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>, vol. 68, Elsevier, 2018, pp. 119–33, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” <i>Computational Geometry: Theory and Applications</i>, vol. 68. Elsevier, pp. 119–133, 2018.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. 2018;68:119-133. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133."},"day":"01","status":"public","ec_funded":1,"date_updated":"2025-04-15T08:37:54Z","publisher":"Elsevier","department":[{"_id":"HeEd"}],"date_published":"2018-03-01T00:00:00Z","language":[{"iso":"eng"}],"month":"03","file_date_updated":"2020-07-14T12:46:38Z","oa":1,"isi":1,"scopus_import":"1","_id":"530","publist_id":"7289","type":"journal_article","intvolume":"        68","oa_version":"Preprint","ddc":["000"],"has_accepted_license":"1","file":[{"creator":"dernst","date_created":"2019-02-12T06:47:52Z","file_name":"2018_Edelsbrunner.pdf","content_type":"application/pdf","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","relation":"main_file","access_level":"open_access","file_size":708357,"date_updated":"2020-07-14T12:46:38Z","file_id":"5953"}],"quality_controlled":"1","corr_author":"1","publication":"Computational Geometry: Theory and Applications","doi":"10.1016/j.comgeo.2017.06.014","date_created":"2018-12-11T11:46:59Z","year":"2018","title":"Multiple covers with balls I: Inclusion–exclusion","external_id":{"isi":["000415778300010"]},"publication_status":"published","abstract":[{"text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.","lang":"eng"}],"article_processing_charge":"No","page":"119 - 133","volume":68,"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2018-11-01T00:00:00Z","month":"11","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:53:54Z","department":[{"_id":"DaAl"}],"publisher":"Springer","isi":1,"file_date_updated":"2020-07-14T12:46:38Z","oa":1,"publist_id":"7281","scopus_import":"1","_id":"536","intvolume":"        31","oa_version":"Published Version","type":"journal_article","citation":{"ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. <i>Distributed Computing</i>. 2018;31(6):489-501. doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” <i>Distributed Computing</i>, vol. 31, no. 6. Springer, pp. 489–501, 2018.","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:<a href=\"https://doi.org/10.1007/s00446-017-0315-1\">10.1007/s00446-017-0315-1</a>.","apa":"Alistarh, D.-A., Aspnes, J., King, V., &#38; Saia, J. (2018). Communication-efficient randomized consensus. <i>Distributed Computing</i>. Springer. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” <i>Distributed Computing</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00446-017-0315-1\">https://doi.org/10.1007/s00446-017-0315-1</a>."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"status":"public","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"title":"Communication-efficient randomized consensus","article_processing_charge":"Yes (via OA deal)","page":"489-501","publication_status":"published","external_id":{"isi":["000443832300005"]},"abstract":[{"lang":"eng","text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"full_name":"King, Valerie","first_name":"Valerie","last_name":"King"},{"first_name":"Jared","last_name":"Saia","full_name":"Saia, Jared"}],"volume":31,"has_accepted_license":"1","ddc":["000"],"corr_author":"1","file":[{"creator":"dernst","file_name":"2017_DistribComp_Alistarh.pdf","content_type":"application/pdf","date_created":"2019-01-22T07:25:51Z","file_size":595707,"date_updated":"2020-07-14T12:46:38Z","access_level":"open_access","relation":"main_file","checksum":"69b46e537acdcac745237ddb853fcbb5","file_id":"5867"}],"quality_controlled":"1","doi":"10.1007/s00446-017-0315-1","publication_identifier":{"issn":["0178-2770"]},"issue":"6","publication":"Distributed Computing","date_created":"2018-12-11T11:47:01Z","year":"2018"},{"publication":"Developmental Cell","issue":"1","doi":"10.1016/j.devcel.2018.09.014","year":"2018","date_created":"2018-12-11T11:44:23Z","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014","open_access":"1"}],"quality_controlled":"1","volume":47,"author":[{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","first_name":"Diana C"},{"last_name":"Bellaïche","first_name":"Yohanns","full_name":"Bellaïche, Yohanns"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","abstract":[{"text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000446579900002"]},"page":"3 - 19","article_processing_charge":"No","day":"08","status":"public","OA_type":"free access","citation":{"apa":"Nunes Pinheiro, D. C., &#38; Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>.","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” <i>Developmental Cell</i>, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. 2018;47(1):3-19. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19."},"_id":"54","scopus_import":"1","publist_id":"8000","type":"journal_article","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","article_type":"review","oa_version":"Published Version","intvolume":"        47","department":[{"_id":"CaHe"}],"publisher":"Cell Press","date_updated":"2026-06-18T18:52:56Z","language":[{"iso":"eng"}],"month":"10","date_published":"2018-10-08T00:00:00Z","oa":1,"isi":1},{"_id":"543","scopus_import":"1","publist_id":"7273","type":"journal_article","intvolume":"       115","oa_version":"Submitted Version","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"date_updated":"2025-05-14T10:55:59Z","month":"01","language":[{"iso":"eng"}],"date_published":"2018-01-02T00:00:00Z","oa":1,"isi":1,"status":"public","day":"02","project":[{"grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"citation":{"mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America. 115(1), 186–191.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","short":"M.J. Chalk, O. Marre, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 186–191."},"volume":115,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","first_name":"Matthew J","last_name":"Chalk"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper"}],"title":"Toward a unified theory of efficient, predictive, and sparse coding","abstract":[{"text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000419128700049"]},"page":"186 - 191","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"1","doi":"10.1073/pnas.1711114115","year":"2018","date_created":"2018-12-11T11:47:04Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"quality_controlled":"1","corr_author":"1"},{"volume":48,"author":[{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Neural stem cells in neuropsychiatric disorders","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."}],"publication_status":"published","external_id":{"isi":["000427101600018"]},"page":"131 - 138","article_processing_charge":"No","publication":"Current Opinion in Neurobiology","issue":"2","doi":"10.1016/j.conb.2017.12.005","year":"2018","date_created":"2018-12-11T11:47:06Z","quality_controlled":"1","corr_author":"1","_id":"546","scopus_import":"1","publist_id":"7268","type":"journal_article","intvolume":"        48","oa_version":"None","publisher":"Elsevier","department":[{"_id":"GaNo"}],"date_updated":"2024-10-09T20:58:31Z","language":[{"iso":"eng"}],"month":"02","date_published":"2018-02-01T00:00:00Z","isi":1,"status":"public","day":"01","citation":{"short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","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. <i>Current Opinion in Neurobiology</i>. 2018;48(2):131-138. doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>","apa":"Sacco, R., Cacci, E., &#38; Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>."}},{"title":"Protection against the lethal side effects of social immunity in ants","external_id":{"isi":["000446693400008"]},"publication_status":"published","abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"article_processing_charge":"No","page":"R1139 - R1140","volume":28,"author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull"},{"last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"quality_controlled":"1","publication":"Current Biology","doi":"10.1016/j.cub.2018.08.063","issue":"19","date_created":"2018-12-11T11:44:23Z","year":"2018","date_updated":"2026-06-18T18:53:43Z","department":[{"_id":"SyCr"}],"publisher":"Cell Press","date_published":"2018-10-08T00:00:00Z","language":[{"iso":"eng"}],"month":"10","oa":1,"isi":1,"scopus_import":"1","_id":"55","publist_id":"7999","type":"journal_article","oa_version":"Published Version","intvolume":"        28","article_type":"original","citation":{"apa":"Pull, C., Metzler, S., Naderlinger, E., &#38; Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>.","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” <i>Current Biology</i>, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. 2018;28(19):R1139-R1140. doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>"},"day":"08","status":"public"},{"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"citation":{"mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>.","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. 2018;360(1):347-403. doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1. Springer, pp. 347–403, 2018.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403."},"status":"public","day":"01","arxiv":1,"publisher":"Springer","department":[{"_id":"RoSe"}],"date_updated":"2025-07-10T11:52:52Z","language":[{"iso":"eng"}],"month":"05","date_published":"2018-05-01T00:00:00Z","oa":1,"_id":"554","scopus_import":"1","publist_id":"7260","type":"journal_article","oa_version":"Submitted Version","intvolume":"       360","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"quality_controlled":"1","publication":"Communications in Mathematical Physics","issue":"1","publication_identifier":{"issn":["0010-3616"]},"doi":"10.1007/s00220-017-3064-x","year":"2018","date_created":"2018-12-11T11:47:09Z","title":"The Bogoliubov free energy functional II: The dilute Limit","abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"external_id":{"arxiv":["1511.05953"]},"publication_status":"published","page":"347-403","article_processing_charge":"No","volume":360,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"},{"last_name":"Reuvers","first_name":"Robin","full_name":"Reuvers, Robin"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}]},{"title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","page":"65 - 74","article_processing_charge":"No","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"external_id":{"isi":["000443661300011"]},"publication_status":"published","author":[{"last_name":"Richter","first_name":"Ralf","full_name":"Richter, Ralf"},{"last_name":"Baranova","first_name":"Natalia","full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"last_name":"Day","first_name":"Anthony","full_name":"Day, Anthony"},{"full_name":"Kwok, Jessica","first_name":"Jessica","last_name":"Kwok"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":50,"main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.sbi.2017.12.002","publication":"Current Opinion in Structural Biology","year":"2018","date_created":"2018-12-11T11:47:09Z","language":[{"iso":"eng"}],"month":"06","date_published":"2018-06-01T00:00:00Z","department":[{"_id":"MaLo"}],"publisher":"Elsevier","date_updated":"2023-09-11T14:07:03Z","isi":1,"oa":1,"publist_id":"7259","_id":"555","scopus_import":"1","article_type":"original","intvolume":"        50","oa_version":"Submitted Version","type":"journal_article","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","citation":{"ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>, vol. 50, Elsevier, 2018, pp. 65–74, doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>.","apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>."},"day":"01","status":"public"},{"has_accepted_license":"1","ddc":["500"],"file":[{"access_level":"open_access","checksum":"0c38abe73569b7166b7487ad5d23cc68","relation":"main_file","file_size":3084674,"date_updated":"2020-07-14T12:47:03Z","file_id":"5866","creator":"dernst","date_created":"2019-01-21T15:18:55Z","content_type":"application/pdf","file_name":"2018_Annales_Betea.pdf"}],"quality_controlled":"1","doi":"10.1007/s00023-018-0723-1","publication_identifier":{"issn":["1424-0637"]},"issue":"12","publication":"Annales Henri Poincare","date_created":"2018-12-11T11:47:09Z","year":"2018","title":"The free boundary Schur process and applications I","article_processing_charge":"Yes (via OA deal)","page":"3663-3742","external_id":{"isi":["000450487900003"],"arxiv":["1704.05809"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Betea, Dan","first_name":"Dan","last_name":"Betea"},{"first_name":"Jeremie","last_name":"Bouttier","full_name":"Bouttier, Jeremie"},{"first_name":"Peter","last_name":"Nejjar","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter"},{"full_name":"Vuletic, Mirjana","first_name":"Mirjana","last_name":"Vuletic"}],"volume":19,"citation":{"ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. 2018;19(12):3663-3742. doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” <i>Annales Henri Poincare</i>, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>.","apa":"Betea, D., Bouttier, J., Nejjar, P., &#38; Vuletic, M. (2018). The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>"},"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"status":"public","day":"13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_published":"2018-11-13T00:00:00Z","month":"11","language":[{"iso":"eng"}],"date_updated":"2025-09-18T07:34:29Z","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"arxiv":1,"publisher":"Springer Nature","isi":1,"file_date_updated":"2020-07-14T12:47:03Z","oa":1,"publist_id":"7258","scopus_import":"1","_id":"556","oa_version":"Published Version","intvolume":"        19","article_type":"original","type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","first_name":"Nela","last_name":"Nikolic"}],"oa_version":"Published Version","type":"research_data","publist_id":"7385","_id":"5569","related_material":{"record":[{"status":"public","id":"438","relation":"research_paper"}]},"article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/","file_date_updated":"2020-07-14T12:47:04Z","oa":1,"abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"keyword":["microscopy","microfluidics"],"date_published":"2018-02-07T00:00:00Z","month":"02","title":"Time-lapse microscopy data","date_updated":"2026-04-16T12:20:36Z","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-12T12:31:35Z","datarep_id":"74","year":"2018","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"doi":"10.15479/AT:ISTA:74","status":"public","day":"07","citation":{"apa":"Bergmiller, T., &#38; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>.","mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018).","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>."},"file":[{"access_level":"open_access","checksum":"61ebb92213cfffeba3ddbaff984b81af","relation":"main_file","file_size":3558703796,"date_updated":"2020-07-14T12:47:04Z","file_id":"5637","creator":"system","date_created":"2018-12-12T13:04:39Z","content_type":"application/zip","file_name":"IST-2018-74-v1+2_15-11-05.zip"},{"relation":"main_file","checksum":"bf26649af310ef6892d68576515cde6d","access_level":"open_access","date_updated":"2020-07-14T12:47:04Z","file_size":1830422606,"file_id":"5638","creator":"system","date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","content_type":"application/zip"},{"file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","relation":"main_file","access_level":"open_access","file_id":"5639","creator":"system","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","content_type":"application/zip","date_created":"2018-12-12T13:05:11Z"}],"has_accepted_license":"1","ddc":["579"]},{"citation":{"mla":"Alhaija, Hassan, et al. <i>Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow</i>. 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Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","short":"T. Ellis, (2018).","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018."},"has_accepted_license":"1","type":"research_data","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas"}],"related_material":{"record":[{"relation":"research_paper","id":"286","status":"public"}]},"_id":"5583","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:47:07Z","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"date_updated":"2025-04-15T07:11:03Z","month":"02","title":"Data and Python scripts supporting Python package FAPS","date_published":"2018-02-12T00:00:00Z"},{"_id":"5584","related_material":{"record":[{"relation":"used_in_publication","id":"292","status":"public"}]},"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"last_name":"Deny","first_name":"Stephane","full_name":"Deny, Stephane"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"full_name":"Botella-Soler, Vicente","first_name":"Vicente","last_name":"Botella-Soler"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2025-04-15T08:18:24Z","month":"03","title":"Nonlinear decoding of a complex movie from the mammalian retina","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"date_published":"2018-03-29T00:00:00Z","abstract":[{"lang":"eng","text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. 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S., &#38; Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>","mla":"Deny, Stephane, et al. <i>Nonlinear Decoding of a Complex Movie from the Mammalian Retina</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>."}},{"file":[{"date_created":"2018-12-12T13:05:13Z","content_type":"application/zip","file_name":"IST-2018-111-v1+1_CODES.zip","creator":"system","file_id":"5641","relation":"main_file","checksum":"97992e3e8cf8544ec985a48971708726","access_level":"open_access","date_updated":"2020-07-14T12:47:08Z","file_size":14376}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"citation":{"ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>","short":"D. De Martino, G. Tkačik, (2018).","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","mla":"De Martino, Daniele, and Gašper Tkačik. <i>Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>.","apa":"De Martino, D., &#38; Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>"},"ddc":["530"],"has_accepted_license":"1","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"year":"2018","date_created":"2018-12-12T12:31:41Z","datarep_id":"111","day":"21","status":"public","doi":"10.15479/AT:ISTA:62","oa":1,"abstract":[{"lang":"eng","text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra  (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and  \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015)."}],"file_date_updated":"2020-07-14T12:47:08Z","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2025-04-15T06:50:08Z","month":"09","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","date_published":"2018-09-21T00:00:00Z","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"type":"research_data","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"_id":"5587"}]