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Tomanek, (2019).","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019."},"department":[{"_id":"CaGu"}],"date_created":"2019-11-13T09:07:31Z","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"page":"423-433.e1-e3","isi":1,"type":"journal_article","oa":1,"publication_status":"published","article_processing_charge":"No","year":"2019","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":4238460,"creator":"dernst","file_name":"2019_CellSystems_Lukacisin.pdf","checksum":"7a11d6c2f9523d65b049512d61733178","date_created":"2019-11-15T10:57:42Z","relation":"main_file","date_updated":"2020-07-14T12:47:48Z","file_id":"7027"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-27T00:00:00Z","date_created":"2019-11-15T10:51:42Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information."}],"publisher":"Cell Press","language":[{"iso":"eng"}],"intvolume":" 9","issue":"5","status":"public","ddc":["570"],"month":"11","publication":"Cell Systems","acknowledged_ssus":[{"_id":"LifeSc"}],"day":"27","article_type":"original","publication_identifier":{"issn":["2405-4712"]},"file_date_updated":"2020-07-14T12:47:48Z","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"isi":["000499495400003"]},"author":[{"first_name":"Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin"},{"first_name":"Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","date_updated":"2025-04-15T08:09:37Z","department":[{"_id":"ToBo"}],"scopus_import":"1","volume":9,"project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004","apa":"Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004","ista":"Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3.","ieee":"M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019.","mla":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","chicago":"Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.cels.2019.10.004","_id":"7026","oa_version":"Published Version","quality_controlled":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-10-29T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","isi":1,"ec_funded":1,"type":"journal_article","oa":1,"page":"1267-1279","status":"public","publication":"Combinatorica","month":"10","issue":"6","language":[{"iso":"eng"}],"intvolume":" 39","abstract":[{"text":"We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.","lang":"eng"}],"date_created":"2019-11-18T14:29:50Z","publisher":"Springer Nature","date_updated":"2025-04-14T13:52:37Z","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4","author":[{"first_name":"Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"}],"external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"publication_identifier":{"eissn":["1439-6912"],"issn":["0209-9683"]},"article_type":"original","day":"29","arxiv":1,"_id":"7034","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00493-019-3905-7","citation":{"ama":"Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7","apa":"Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7","ista":"Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279.","mla":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7.","ieee":"R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7."},"scopus_import":"1","department":[{"_id":"UlWa"}],"volume":39},{"department":[{"_id":"LaEr"}],"volume":2125,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41.","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.","mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019."},"_id":"7035","main_file_link":[{"url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html","open_access":"1"}],"oa_version":"Submitted Version","quality_controlled":"1","acknowledgement":"This paper is part of a long term collaboration investigating the isometric structure of Wasserstein\r\nspaces. The authors would like to thank the warm hospitality and generosity of László Erdós and his\r\ngroup at Institute of Science and Technology Austria.\r\nT. Titkos wants to thank Oriental Business and Innovation Center ‐ OBIC for providing financial\r\nsupport to participate in the symposium at the Kyoto RIMS.\r\nGy. P. Gehér was supported by the Leverhulme Trust Early Career Fellowship (ECF‐2018‐125),\r\nand also by the Hungarian National Research, Development and Innovation Office (K115383). T.\r\nTitkos was supported by the Hungarian National Research, Development and Innovation Office‐ NKFIH\r\n(PD128374), by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences, and by the\r\nUNKP‐18‐4‐BGE‐3 New National Excellence Program of the Ministry of Human Capacities. D. Virosztek\r\nwas supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project\r\ncode IC1027FELL01 ) and partially supported by the Hungarian National Research, Development and\r\nInnovation Office NKFIH (grant no. K124152 and grant no. KH129601)","day":"30","conference":{"end_date":"2019-01-30","name":"Research on isometries as preserver problems and related topics","location":"Kyoto, Japan","start_date":"2019-01-28"},"OA_place":"repository","author":[{"full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal","last_name":"Geher"},{"full_name":"Titkos, Tamas","first_name":"Tamas","last_name":"Titkos"},{"last_name":"Virosztek","orcid":"0000-0003-1109-5511","first_name":"Daniel","full_name":"Virosztek, Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-06-30T09:55:30Z","title":"Dirac masses and isometric rigidity","abstract":[{"lang":"eng","text":"The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question."}],"date_created":"2019-11-18T15:39:53Z","publisher":"Research Institute for Mathematical Sciences, Kyoto University","language":[{"iso":"eng"}],"OA_type":"green","intvolume":" 2125","publication":"Kyoto RIMS Kôkyûroku","corr_author":"1","month":"01","status":"public","page":"34-41","ec_funded":1,"type":"conference","oa":1,"year":"2019","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-01-30T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"101116","date_published":"2019-10-17T00:00:00Z","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:48Z","file_id":"7087","content_type":"application/pdf","access_level":"open_access","file_size":2453220,"checksum":"142fe7b3e37d8e916071743bb194360d","creator":"dernst","file_name":"2019_APL_Shirer.pdf","relation":"main_file","date_created":"2019-11-20T12:27:01Z"}],"type":"journal_article","oa":1,"publication":"APL Materials","ddc":["530"],"month":"10","status":"public","issue":"10","language":[{"iso":"eng"}],"intvolume":" 7","has_accepted_license":"1","date_created":"2019-11-19T12:52:43Z","abstract":[{"text":"A recent class of topological nodal-line semimetals with the general formula MSiX (M = Zr, Hf and X = S, Se, Te) has attracted much experimental and theoretical interest due to their properties, particularly their large magnetoresistances and high carrier mobilities. The plateletlike nature of the MSiX crystals and their extremely low residual resistivities make measurements of the resistivity along the [001] direction extremely challenging. To accomplish such measurements, microstructures of single crystals were prepared using focused ion beam techniques. Microstructures prepared in this manner have very well-defined geometries and maintain their high crystal quality, verified by the observations of quantum oscillations. We present magnetoresistance and quantum oscillation data for currents applied along both [001] and [100] in ZrSiS and ZrSiSe, which are consistent with the nontrivial topology of the Dirac line-node, as determined by a measured π Berry phase. Surprisingly, we find that, despite the three dimensional nature of both the Fermi surfaces of ZrSiS and ZrSiSe, both the resistivity anisotropy under applied magnetic fields and the in-plane angular dependent magnetoresistance differ considerably between the two compounds. Finally, we discuss the role microstructuring can play in the study of these materials and our ability to make these microstructures free-standing.","lang":"eng"}],"publisher":"AIP","date_updated":"2021-01-12T08:11:35Z","title":"Out-of-plane transport in ZrSiS and ZrSiSe microstructures","author":[{"full_name":"Shirer, Kent R.","last_name":"Shirer","first_name":"Kent R."},{"first_name":"Kimberly A","orcid":"0000-0001-9760-3147","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"},{"full_name":"Zimmerling, Tino","first_name":"Tino","last_name":"Zimmerling"},{"full_name":"Bachmann, Maja D.","last_name":"Bachmann","first_name":"Maja D."},{"full_name":"König, Markus","last_name":"König","first_name":"Markus"},{"last_name":"Moll","first_name":"Philip J. W.","full_name":"Moll, Philip J. W."},{"last_name":"Schoop","first_name":"Leslie","full_name":"Schoop, Leslie"},{"full_name":"Mackenzie, Andrew P.","last_name":"Mackenzie","first_name":"Andrew P."}],"publication_identifier":{"issn":["2166-532X"]},"article_type":"original","file_date_updated":"2020-07-14T12:47:48Z","day":"17","extern":"1","_id":"7055","oa_version":"Published Version","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1063/1.5124568","citation":{"apa":"Shirer, K. R., Modic, K. A., Zimmerling, T., Bachmann, M. D., König, M., Moll, P. J. W., … Mackenzie, A. P. (2019). Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. AIP. https://doi.org/10.1063/1.5124568","ama":"Shirer KR, Modic KA, Zimmerling T, et al. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 2019;7(10). doi:10.1063/1.5124568","ista":"Shirer KR, Modic KA, Zimmerling T, Bachmann MD, König M, Moll PJW, Schoop L, Mackenzie AP. 2019. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 7(10), 101116.","ieee":"K. R. Shirer et al., “Out-of-plane transport in ZrSiS and ZrSiSe microstructures,” APL Materials, vol. 7, no. 10. AIP, 2019.","mla":"Shirer, Kent R., et al. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials, vol. 7, no. 10, 101116, AIP, 2019, doi:10.1063/1.5124568.","short":"K.R. Shirer, K.A. Modic, T. Zimmerling, M.D. Bachmann, M. König, P.J.W. Moll, L. Schoop, A.P. Mackenzie, APL Materials 7 (2019).","chicago":"Shirer, Kent R., Kimberly A Modic, Tino Zimmerling, Maja D. Bachmann, Markus König, Philip J. W. Moll, Leslie Schoop, and Andrew P. Mackenzie. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials. AIP, 2019. https://doi.org/10.1063/1.5124568."},"volume":7},{"oa":1,"type":"journal_article","article_number":"485705","date_published":"2019-09-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","article_processing_charge":"No","publication_status":"published","intvolume":" 31","language":[{"iso":"eng"}],"publisher":"IOP Publishing","abstract":[{"lang":"eng","text":"In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have investigated a highly overdoped composition (x = 0.56), prepared by a high-pressure, high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition at T N = 120 K, well above the one at lower doping (0.15 < x < 0.27).\r\n\r\nBelow the onset of long-range magnetic order at T N, the electrical resistivity is strongly reduced and is dominated by electron–electron interactions, as evident from its temperature dependence. The Seebeck coefficient shows a clear metallic behavior as in narrow band conductors. The temperature dependence of the Hall coefficient and the violation of Kohler's rule agree with the multiband character of the material. No superconductivity was observed down to 1.8 K. The success of the high-pressure synthesis encourages further investigations of the so far only partially explored phase diagram in this family of Iron-based high temperature superconductors.\r\n"}],"date_created":"2019-11-19T12:56:17Z","publication":"Journal of Physics: Condensed Matter","status":"public","month":"09","issue":"48","external_id":{"arxiv":["1905.08640"]},"arxiv":1,"article_type":"original","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"day":"03","date_updated":"2021-01-12T08:11:35Z","title":"Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2","author":[{"full_name":"Martino, Edoardo","first_name":"Edoardo","last_name":"Martino"},{"last_name":"Bachmann","first_name":"Maja D","full_name":"Bachmann, Maja D"},{"last_name":"Rossi","first_name":"Lidia","full_name":"Rossi, Lidia"},{"full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147"},{"full_name":"Zivkovic, Ivica","last_name":"Zivkovic","first_name":"Ivica"},{"first_name":"Henrik M","last_name":"Rønnow","full_name":"Rønnow, Henrik M"},{"full_name":"Moll, Philip J W","first_name":"Philip J W","last_name":"Moll"},{"first_name":"Ana","last_name":"Akrap","full_name":"Akrap, Ana"},{"last_name":"Forró","first_name":"László","full_name":"Forró, László"},{"full_name":"Katrych, Sergiy","first_name":"Sergiy","last_name":"Katrych"}],"citation":{"chicago":"Martino, Edoardo, Maja D Bachmann, Lidia Rossi, Kimberly A Modic, Ivica Zivkovic, Henrik M Rønnow, Philip J W Moll, Ana Akrap, László Forró, and Sergiy Katrych. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter. IOP Publishing, 2019. https://doi.org/10.1088/1361-648x/ab3b43.","short":"E. Martino, M.D. Bachmann, L. Rossi, K.A. Modic, I. Zivkovic, H.M. Rønnow, P.J.W. Moll, A. Akrap, L. Forró, S. Katrych, Journal of Physics: Condensed Matter 31 (2019).","ieee":"E. Martino et al., “Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2,” Journal of Physics: Condensed Matter, vol. 31, no. 48. IOP Publishing, 2019.","mla":"Martino, Edoardo, et al. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter, vol. 31, no. 48, 485705, IOP Publishing, 2019, doi:10.1088/1361-648x/ab3b43.","ama":"Martino E, Bachmann MD, Rossi L, et al. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 2019;31(48). doi:10.1088/1361-648x/ab3b43","ista":"Martino E, Bachmann MD, Rossi L, Modic KA, Zivkovic I, Rønnow HM, Moll PJW, Akrap A, Forró L, Katrych S. 2019. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 31(48), 485705.","apa":"Martino, E., Bachmann, M. D., Rossi, L., Modic, K. A., Zivkovic, I., Rønnow, H. M., … Katrych, S. (2019). Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648x/ab3b43"},"doi":"10.1088/1361-648x/ab3b43","volume":31,"main_file_link":[{"url":"https://arxiv.org/abs/1905.08640","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","_id":"7056","extern":"1"},{"oa_version":"Published Version","quality_controlled":"1","_id":"7057","extern":"1","doi":"10.1038/s41598-018-38161-7","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Modic, Kimberly A, Tobias Meng, Filip Ronning, Eric D. Bauer, Philip J. W. Moll, and B. J. Ramshaw. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-018-38161-7.","short":"K.A. Modic, T. Meng, F. Ronning, E.D. Bauer, P.J.W. Moll, B.J. Ramshaw, Scientific Reports 9 (2019).","ieee":"K. A. Modic, T. Meng, F. Ronning, E. D. Bauer, P. J. W. Moll, and B. J. Ramshaw, “Thermodynamic signatures of Weyl fermions in NbP,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019.","mla":"Modic, Kimberly A., et al. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports, vol. 9, no. 1, 2095, Springer Nature, 2019, doi:10.1038/s41598-018-38161-7.","apa":"Modic, K. A., Meng, T., Ronning, F., Bauer, E. D., Moll, P. J. W., & Ramshaw, B. J. (2019). Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-38161-7","ista":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. 2019. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 9(1), 2095.","ama":"Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-38161-7"},"volume":9,"date_updated":"2021-01-12T08:11:36Z","title":"Thermodynamic signatures of Weyl fermions in NbP","author":[{"orcid":"0000-0001-9760-3147","last_name":"Modic","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"},{"full_name":"Meng, Tobias","first_name":"Tobias","last_name":"Meng"},{"full_name":"Ronning, Filip","first_name":"Filip","last_name":"Ronning"},{"last_name":"Bauer","first_name":"Eric D.","full_name":"Bauer, Eric D."},{"full_name":"Moll, Philip J. W.","first_name":"Philip J. W.","last_name":"Moll"},{"full_name":"Ramshaw, B. J.","last_name":"Ramshaw","first_name":"B. J."}],"publication_identifier":{"issn":["2045-2322"]},"file_date_updated":"2020-07-14T12:47:48Z","article_type":"original","day":"14","publication":"Scientific Reports","status":"public","month":"02","ddc":["530"],"issue":"1","intvolume":" 9","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_created":"2019-11-19T13:00:35Z","abstract":[{"text":"We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field.","lang":"eng"}],"has_accepted_license":"1","date_published":"2019-02-14T00:00:00Z","article_number":"2095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:48Z","file_id":"7086","content_type":"application/pdf","access_level":"open_access","file_size":3256400,"creator":"dernst","file_name":"2019_ScientificReports_Modic.pdf","checksum":"3b5a7b316e1ff22aa0f89e8d1f1ace91","relation":"main_file","date_created":"2019-11-20T12:24:13Z"}],"article_processing_charge":"No","year":"2019","publication_status":"published","oa":1,"type":"journal_article"},{"oa_version":"Published Version","quality_controlled":"1","_id":"7093","volume":10,"scopus_import":"1","department":[{"_id":"UlWa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. Computational Geometry Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5."},"doi":"10.20382/JOGC.V10I2A5","author":[{"orcid":"0000-0002-5445-5057","last_name":"Huszár","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"date_updated":"2026-04-08T07:21:27Z","title":"On the treewidth of triangulated 3-manifolds","arxiv":1,"publication_identifier":{"issn":["1920-180X"]},"article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"285","status":"public"},{"id":"8032","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2020-07-14T12:47:49Z","day":"01","external_id":{"arxiv":["1712.00434"]},"issue":"2","ddc":["514"],"status":"public","month":"11","publication":"Journal of Computational Geometry","publisher":"Computational Geometry Laborartoy","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))."}],"has_accepted_license":"1","date_created":"2019-11-23T12:14:09Z","intvolume":" 10","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:49Z","file_id":"7094","access_level":"open_access","content_type":"application/pdf","file_size":857590,"creator":"khuszar","checksum":"c872d590d38d538404782bca20c4c3f5","file_name":"479-1917-1-PB.pdf","date_created":"2019-11-23T12:35:16Z","relation":"main_file"}],"year":"2019","article_processing_charge":"No","publication_status":"published","date_published":"2019-11-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"70–98","oa":1,"type":"journal_article"},{"_id":"7095","oa_version":"Published Version","quality_controlled":"1","citation":{"ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” Scientific Reports, vol. 9. Springer Nature, 2019.","mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer Nature, 2019, doi:10.1038/s41598-019-53049-w.","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 2019;9. doi:10.1038/s41598-019-53049-w","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565.","chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41598-019-53049-w","department":[{"_id":"SaSi"}],"scopus_import":"1","volume":9,"date_updated":"2023-08-30T07:26:54Z","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","first_name":"Margaret E"},{"full_name":"Grosser, J. A.","last_name":"Grosser","first_name":"J. A."},{"full_name":"Fehrman, R. L.","first_name":"R. L.","last_name":"Fehrman"},{"full_name":"Schlamp, C. L.","last_name":"Schlamp","first_name":"C. L."},{"full_name":"Nickells, R. W.","last_name":"Nickells","first_name":"R. W."}],"external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"article_type":"original","file_date_updated":"2020-07-14T12:47:49Z","publication_identifier":{"eissn":["2045-2322"]},"day":"12","month":"11","ddc":["570"],"publication":"Scientific Reports","status":"public","language":[{"iso":"eng"}],"intvolume":" 9","has_accepted_license":"1","date_created":"2019-11-25T07:45:17Z","pmid":1,"abstract":[{"lang":"eng","text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells."}],"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-12T00:00:00Z","article_number":"16565","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":6467393,"checksum":"9ab397ed9c1c454b34bffb8cc863d734","file_name":"2019_ScientificReports_Maes.pdf","creator":"dernst","date_created":"2019-11-25T07:49:52Z","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","file_id":"7096"}],"isi":1,"type":"journal_article","oa":1},{"publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:47:49Z","file_id":"7098","access_level":"open_access","content_type":"application/pdf","file_size":2626069,"checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","creator":"dernst","file_name":"2019_CommunicBiology_Nagano.pdf","date_created":"2019-11-25T07:58:05Z","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-15T00:00:00Z","article_number":"419","isi":1,"type":"journal_article","oa":1,"issue":"1","status":"public","publication":"Communications Biology","month":"11","ddc":["570"],"date_created":"2019-11-25T07:55:01Z","abstract":[{"text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway.","lang":"eng"}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 2","author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","date_updated":"2023-08-30T07:27:55Z","day":"15","publication_identifier":{"issn":["2399-3642"]},"file_date_updated":"2020-07-14T12:47:49Z","article_type":"original","external_id":{"isi":["000496767800005"]},"_id":"7097","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"DaSi"}],"scopus_import":"1","volume":2,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” Communications Biology, vol. 2, no. 1. Springer Nature, 2019.","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer Nature, 2019, doi:10.1038/s42003-019-0670-5.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2019;2(1). doi:10.1038/s42003-019-0670-5","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419.","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5.","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019)."},"doi":"10.1038/s42003-019-0670-5"},{"page":"781-794.e4","type":"journal_article","isi":1,"oa":1,"publication_status":"published","article_processing_charge":"No","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-11-20T00:00:00Z","date_created":"2019-11-25T08:02:39Z","has_accepted_license":"1","pmid":1,"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":" 104","issue":"4","status":"public","publication":"Neuron","month":"11","ddc":["571","599"],"day":"20","article_type":"original","acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","publication_identifier":{"issn":["0896-6273"]},"external_id":{"pmid":["31543297"],"isi":["000497963500017"]},"author":[{"last_name":"Kasugai","first_name":"Yu","full_name":"Kasugai, Yu"},{"full_name":"Vogel, Elisabeth","last_name":"Vogel","first_name":"Elisabeth"},{"last_name":"Hörtnagl","first_name":"Heide","full_name":"Hörtnagl, Heide"},{"last_name":"Schönherr","first_name":"Sabine","full_name":"Schönherr, Sabine"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"full_name":"Hauschild, Markus","first_name":"Markus","last_name":"Hauschild"},{"full_name":"Göbel, Georg","first_name":"Georg","last_name":"Göbel"},{"full_name":"Milenkovic, Ivan","first_name":"Ivan","last_name":"Milenkovic"},{"first_name":"Yvan","last_name":"Peterschmitt","full_name":"Peterschmitt, Yvan"},{"full_name":"Tasan, Ramon","last_name":"Tasan","first_name":"Ramon"},{"last_name":"Sperk","first_name":"Günther","full_name":"Sperk, Günther"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Sieghart, Werner","last_name":"Sieghart","first_name":"Werner"},{"full_name":"Singewald, Nicolas","last_name":"Singewald","first_name":"Nicolas"},{"first_name":"Andreas","last_name":"Lüthi","full_name":"Lüthi, Andreas"},{"first_name":"Francesco","last_name":"Ferraguti","full_name":"Ferraguti, Francesco"}],"title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","date_updated":"2023-08-30T07:28:22Z","department":[{"_id":"RySh"}],"scopus_import":"1","volume":104,"doi":"10.1016/j.neuron.2019.08.013","citation":{"ieee":"Y. Kasugai et al., “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” Neuron, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4.","apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013","ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4. doi:10.1016/j.neuron.2019.08.013","chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.013.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4."},"_id":"7099","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.013","open_access":"1"}]},{"ec_funded":1,"isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"relation":"main_file","date_created":"2019-11-25T08:24:01Z","file_name":"2019_PLOSComBio_Wang.pdf","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","creator":"dernst","file_size":3982516,"content_type":"application/pdf","access_level":"open_access","file_id":"7104","date_updated":"2020-07-14T12:47:49Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e1007268","date_published":"2019-11-01T00:00:00Z","has_accepted_license":"1","date_created":"2019-11-25T08:20:47Z","abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"pmid":1,"publisher":"Public Library of Science","language":[{"iso":"eng"}],"intvolume":" 15","issue":"11","month":"11","status":"public","ddc":["570","000"],"publication":"PLoS Computational Biology","day":"01","file_date_updated":"2020-07-14T12:47:49Z","publication_identifier":{"issn":["1553-7358"]},"article_type":"original","external_id":{"pmid":["31725712"],"isi":["000500976100014"]},"author":[{"full_name":"Wang, Jilin W. J. L.","first_name":"Jilin W. J. L.","last_name":"Wang"},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","first_name":"Fabrizio"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"full_name":"Anaclet, Christelle","last_name":"Anaclet","first_name":"Christelle"},{"last_name":"Ivanov","first_name":"Plamen Ch.","full_name":"Ivanov, Plamen Ch."}],"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","date_updated":"2025-04-14T07:44:06Z","department":[{"_id":"GaTk"}],"scopus_import":"1","volume":15,"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007268.","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pcbi.1007268","_id":"7103","oa_version":"Published Version","quality_controlled":"1"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"oa_version":"Submitted Version","quality_controlled":"1","_id":"7105","citation":{"chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","ieee":"L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5"},"doi":"10.1038/s41556-019-0411-5","volume":21,"department":[{"_id":"MiSi"}],"scopus_import":"1","date_updated":"2023-09-06T11:08:52Z","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","author":[{"full_name":"Yolland, Lawrence","last_name":"Yolland","first_name":"Lawrence"},{"first_name":"Mubarik","last_name":"Burki","full_name":"Burki, Mubarik"},{"full_name":"Marcotti, Stefania","first_name":"Stefania","last_name":"Marcotti"},{"last_name":"Luchici","first_name":"Andrei","full_name":"Luchici, Andrei"},{"first_name":"Fiona N.","last_name":"Kenny","full_name":"Kenny, Fiona N."},{"last_name":"Davis","first_name":"John Robert","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","first_name":"Eduardo","last_name":"Serna-Morales"},{"last_name":"Müller","first_name":"Jan","full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"full_name":"Davidson, Andrew","first_name":"Andrew","last_name":"Davidson"},{"first_name":"Will","last_name":"Wood","full_name":"Wood, Will"},{"last_name":"Schumacher","first_name":"Linus J.","full_name":"Schumacher, Linus J."},{"last_name":"Endres","first_name":"Robert G.","full_name":"Endres, Robert G."},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"first_name":"Brian M.","last_name":"Stramer","full_name":"Stramer, Brian M."}],"external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"article_type":"original","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"day":"01","month":"11","publication":"Nature Cell Biology","status":"public","issue":"11","intvolume":" 21","language":[{"iso":"eng"}],"publisher":"Springer Nature","pmid":1,"date_created":"2019-11-25T08:55:00Z","abstract":[{"lang":"eng","text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence."}],"date_published":"2019-11-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","year":"2019","publication_status":"published","oa":1,"isi":1,"type":"journal_article","page":"1370-1381"},{"page":"1114-1119","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"success":1,"file_id":"8660","date_updated":"2020-10-14T08:54:49Z","relation":"main_file","date_created":"2020-10-14T08:54:49Z","file_name":"2019_NaturePlants_Skokan_accepted.pdf","creator":"dernst","checksum":"94e0426856aad9a9bd0135d5436efbf1","file_size":1980851,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-11-01T00:00:00Z","date_created":"2019-11-25T09:08:04Z","abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"pmid":1,"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 5","issue":"11","publication":"Nature Plants","status":"public","month":"11","ddc":["580"],"day":"01","file_date_updated":"2020-10-14T08:54:49Z","publication_identifier":{"issn":["2055-0278"]},"article_type":"original","external_id":{"pmid":["31712756"],"isi":["000496526100010"]},"author":[{"last_name":"Skokan","first_name":"Roman","full_name":"Skokan, Roman"},{"first_name":"Eva","last_name":"Medvecká","full_name":"Medvecká, Eva"},{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Müller, Karel","first_name":"Karel","last_name":"Müller"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"last_name":"Karady","first_name":"Michal","full_name":"Karady, Michal"},{"last_name":"Zhang","first_name":"Yuzhou","full_name":"Zhang, Yuzhou"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z.","last_name":"Hammes"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"title":"PIN-driven auxin transport emerged early in streptophyte evolution","date_updated":"2025-04-14T07:45:04Z","department":[{"_id":"JiFr"}],"scopus_import":"1","volume":5,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"doi":"10.1038/s41477-019-0542-5","citation":{"short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5.","ieee":"R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019."},"_id":"7106","oa_version":"Submitted Version","quality_controlled":"1"},{"publisher":"ACM","date_created":"2019-11-26T10:13:59Z","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"intvolume":" 66","language":[{"iso":"eng"}],"issue":"3","publication":"Journal of the ACM","status":"public","month":"06","oa":1,"type":"journal_article","isi":1,"year":"2019","article_processing_charge":"No","publication_status":"published","article_number":"21","date_published":"2019-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":66,"department":[{"_id":"UlWa"}],"scopus_import":"1","doi":"10.1145/3314024","citation":{"mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019)."},"main_file_link":[{"url":"https://arxiv.org/abs/1711.08436","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"7108","arxiv":1,"article_type":"original","related_material":{"record":[{"status":"public","id":"184","relation":"earlier_version"}]},"publication_identifier":{"issn":["0004-5411"]},"day":"01","external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"id":"B593B804-1035-11EA-B4F1-947645A5BB83","full_name":"Patak, Pavel","first_name":"Pavel","last_name":"Patak"},{"first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Tancer","full_name":"Tancer, Martin"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"date_updated":"2025-06-04T07:49:03Z","title":"Shellability is NP-complete"},{"type":"journal_article","oa":1,"page":"2759-2771.e5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-05-28T00:00:00Z","publication_status":"published","article_processing_charge":"Yes","keyword":["cardiomyocyte","cell cycle","Cofilin2","cytoskeleton","Hippo","microRNA","regeneration","YAP"],"year":"2019","file":[{"checksum":"c5d855d07263bfec718673385d0ea2d7","creator":"rcubero","file_name":"torrini_cellreports_2019.pdf","date_created":"2019-11-26T22:30:43Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":4650750,"file_id":"7129","date_updated":"2020-07-14T12:47:50Z"}],"language":[{"iso":"eng"}],"intvolume":" 27","pmid":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation."}],"date_created":"2019-11-26T22:30:07Z","publisher":"Elsevier","month":"05","ddc":["576"],"status":"public","publication":"Cell Reports","issue":"9","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"pmid":["31141697"]},"day":"28","publication_identifier":{"issn":["2211-1247"]},"article_type":"original","file_date_updated":"2020-07-14T12:47:50Z","title":"Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation","date_updated":"2021-01-12T08:11:56Z","author":[{"last_name":"Torrini","first_name":"Consuelo","full_name":"Torrini, Consuelo"},{"orcid":"0000-0003-0002-1867","last_name":"Cubero","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J"},{"first_name":"Ellen","last_name":"Dirkx","full_name":"Dirkx, Ellen"},{"last_name":"Braga","first_name":"Luca","full_name":"Braga, Luca"},{"last_name":"Ali","first_name":"Hashim","full_name":"Ali, Hashim"},{"full_name":"Prosdocimo, Giulia","last_name":"Prosdocimo","first_name":"Giulia"},{"first_name":"Maria Ines","last_name":"Gutierrez","full_name":"Gutierrez, Maria Ines"},{"first_name":"Chiara","last_name":"Collesi","full_name":"Collesi, Chiara"},{"first_name":"Danilo","last_name":"Licastro","full_name":"Licastro, Danilo"},{"full_name":"Zentilin, Lorena","last_name":"Zentilin","first_name":"Lorena"},{"full_name":"Mano, Miguel","first_name":"Miguel","last_name":"Mano"},{"first_name":"Serena","last_name":"Zacchigna","full_name":"Zacchigna, Serena"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"first_name":"Matteo","last_name":"Marsili","full_name":"Marsili, Matteo"},{"first_name":"Areejit","last_name":"Samal","full_name":"Samal, Areejit"},{"last_name":"Giacca","first_name":"Mauro","full_name":"Giacca, Mauro"}],"doi":"10.1016/j.celrep.2019.05.005","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"short":"C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.","chicago":"Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali, Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports. Elsevier, 2019. https://doi.org/10.1016/j.celrep.2019.05.005.","ama":"Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 2019;27(9):2759-2771.e5. doi:10.1016/j.celrep.2019.05.005","apa":"Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G., … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2019.05.005","ista":"Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.","mla":"Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports, vol. 27, no. 9, Elsevier, 2019, p. 2759–2771.e5, doi:10.1016/j.celrep.2019.05.005.","ieee":"C. Torrini et al., “Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation,” Cell Reports, vol. 27, no. 9. Elsevier, p. 2759–2771.e5, 2019."},"volume":27,"_id":"7128","extern":"1","oa_version":"Published Version","quality_controlled":"1"},{"day":"17","article_type":"original","publication_identifier":{"issn":["1742-5468"]},"acknowledgement":"We acknowledge interesting discussions with M Abbott, E Aurell, J Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part, by the ICTP through the OEA-AC-98 (JS).","arxiv":1,"external_id":{"arxiv":["1808.00249"]},"author":[{"first_name":"Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J"},{"full_name":"Jo, Junghyo","first_name":"Junghyo","last_name":"Jo"},{"first_name":"Matteo","last_name":"Marsili","full_name":"Marsili, Matteo"},{"full_name":"Roudi, Yasser","last_name":"Roudi","first_name":"Yasser"},{"full_name":"Song, Juyong","last_name":"Song","first_name":"Juyong"}],"title":"Statistical criticality arises in most informative representations","date_updated":"2021-01-12T08:11:57Z","volume":2019,"doi":"10.1088/1742-5468/ab16c8","citation":{"ista":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063402.","ama":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab16c8","apa":"Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., & Song, J. (2019). Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab16c8","ieee":"R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality arises in most informative representations,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.","mla":"Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative Representations.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:10.1088/1742-5468/ab16c8.","short":"R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","chicago":"Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song. “Statistical Criticality Arises in Most Informative Representations.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab16c8."},"extern":"1","_id":"7130","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.00249"}],"type":"journal_article","oa":1,"publication_status":"published","keyword":["optimization under uncertainty","source coding","large deviation"],"article_processing_charge":"No","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"063402","date_published":"2019-06-17T00:00:00Z","date_created":"2019-11-26T22:36:09Z","abstract":[{"lang":"eng","text":"We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples."}],"publisher":"IOP Publishing","language":[{"iso":"eng"}],"intvolume":" 2019","issue":"6","month":"06","publication":"Journal of Statistical Mechanics: Theory and Experiment","status":"public"},{"doi":"10.1109/isit.2019.8849240","citation":{"short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: 2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240."},"scopus_import":"1","department":[{"_id":"KrPi"}],"_id":"7136","main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","conference":{"end_date":"2019-07-12","start_date":"2019-07-07","name":"ISIT: International Symposium on Information Theory","location":"Paris, France"},"external_id":{"arxiv":["1702.08476"],"isi":["000489100301043"]},"publication_identifier":{"isbn":["9781538692912"]},"day":"01","arxiv":1,"date_updated":"2023-09-06T11:15:41Z","title":"Strong chain rules for min-entropy under few bits spoiled","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej","first_name":"Maciej","last_name":"Skórski"}],"language":[{"iso":"eng"}],"date_created":"2019-11-28T10:19:21Z","abstract":[{"text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|XCell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4","apa":"Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4."},"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"965-966","oa":1,"type":"journal_article","isi":1,"ddc":["580"],"month":"12","publication":"Cell Research","status":"public","publisher":"Springer Nature","date_created":"2019-12-02T12:30:48Z","pmid":1,"abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"intvolume":" 29","language":[{"iso":"eng"}]},{"day":"15","article_type":"original","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"arxiv":1,"external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"author":[{"full_name":"Anselmetti, G. L. R.","last_name":"Anselmetti","first_name":"G. L. R."},{"first_name":"E. A.","last_name":"Martinez","full_name":"Martinez, E. A."},{"full_name":"Ménard, G. C.","last_name":"Ménard","first_name":"G. C."},{"last_name":"Puglia","first_name":"D.","full_name":"Puglia, D."},{"first_name":"F. K.","last_name":"Malinowski","full_name":"Malinowski, F. K."},{"first_name":"J. S.","last_name":"Lee","full_name":"Lee, J. S."},{"full_name":"Choi, S.","first_name":"S.","last_name":"Choi"},{"first_name":"M.","last_name":"Pendharkar","full_name":"Pendharkar, M."},{"last_name":"Palmstrøm","first_name":"C. J.","full_name":"Palmstrøm, C. J."},{"full_name":"Marcus, C. M.","last_name":"Marcus","first_name":"C. M."},{"full_name":"Casparis, L.","last_name":"Casparis","first_name":"L."},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"title":"End-to-end correlated subgap states in hybrid nanowires","date_updated":"2024-02-28T13:13:51Z","scopus_import":"1","department":[{"_id":"AnHi"}],"volume":100,"citation":{"apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.205412","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412","ieee":"G. L. R. Anselmetti et al., “End-to-end correlated subgap states in hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical Society, 2019.","mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:10.1103/physrevb.100.205412.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412."},"doi":"10.1103/physrevb.100.205412","_id":"7145","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.05549"}],"isi":1,"type":"journal_article","oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"205412","date_published":"2019-11-15T00:00:00Z","abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"date_created":"2019-12-04T16:02:25Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":" 100","issue":"20","month":"11","status":"public","publication":"Physical Review B"}]