[{"issue":"6","publication_status":"published","intvolume":"        98","doi":"10.1111/tpj.14301","file":[{"file_name":"2019_PlantJournal_Rakusov.pdf","creator":"dernst","date_created":"2019-04-15T09:38:43Z","date_updated":"2020-07-14T12:47:25Z","file_id":"6304","file_size":1383100,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ad3b5e270b67ba2a45f894ce3be27920"}],"author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"},{"last_name":"Valošek","full_name":"Valošek, Petr","first_name":"Petr","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"oa_version":"Published Version","external_id":{"isi":["000473644100008"],"pmid":["30821050"]},"pmid":1,"_id":"6262","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"page":"1048-1059","scopus_import":"1","date_created":"2019-04-09T08:46:44Z","ec_funded":1,"article_type":"original","abstract":[{"lang":"eng","text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development."}],"publisher":"Wiley","isi":1,"month":"06","publication":"The Plant Journal","status":"public","oa":1,"ddc":["580"],"quality_controlled":"1","publication_identifier":{"eissn":["1365-313x"],"issn":["0960-7412"]},"year":"2019","type":"journal_article","file_date_updated":"2020-07-14T12:47:25Z","date_updated":"2025-04-15T07:48:04Z","day":"01","department":[{"_id":"JiFr"}],"has_accepted_license":"1","date_published":"2019-06-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"volume":98,"title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","citation":{"apa":"Rakusová, H., Han, H., Valošek, P., &#38; Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>.","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. 2019;98(6):1048-1059. doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” <i>The Plant Journal</i>, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>.","ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059."}},{"abstract":[{"text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.","lang":"eng"}],"article_type":"original","publisher":"Elsevier","date_created":"2019-04-11T20:55:01Z","page":"47-59","_id":"6297","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["570"],"quality_controlled":"1","isi":1,"oa":1,"status":"public","publication":"Matrix Biology","month":"05","has_accepted_license":"1","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}],"date_published":"2019-05-01T00:00:00Z","year":"2019","publication_identifier":{"issn":["0945-053X"]},"type":"journal_article","date_updated":"2023-08-25T10:11:28Z","day":"01","file_date_updated":"2020-07-14T12:47:27Z","volume":"78-79","citation":{"chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>","ieee":"H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59."},"title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","doi":"10.1016/j.matbio.2018.12.002","file":[{"file_name":"2018_MatrixBiology_Davies.pdf","creator":"dernst","date_created":"2020-05-14T09:02:07Z","date_updated":"2020-07-14T12:47:27Z","file_size":4444339,"file_id":"7825","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"790878cd78bfc54a147ddcc7c8f286a0"}],"author":[{"last_name":"Davies","full_name":"Davies, Heather S.","first_name":"Heather S."},{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"full_name":"El Amri, Nouha","last_name":"El Amri","first_name":"Nouha"},{"first_name":"Liliane","full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente"},{"first_name":"Claude","full_name":"Verdier, Claude","last_name":"Verdier"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"last_name":"Richter","full_name":"Richter, Ralf P.","first_name":"Ralf P."},{"full_name":"Débarre, Delphine","last_name":"Débarre","first_name":"Delphine"}],"external_id":{"isi":["000468707600005"]}},{"oa_version":"Published Version","author":[{"orcid":"0000-0001-9439-3148","last_name":"Stella","full_name":"Stella, Federico","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","full_name":"Baracskay, Peter"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"doi":"10.1016/j.neuron.2019.01.052","related_material":{"link":[{"url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/","relation":"press_release","description":"News on IST Homepage"}]},"pmid":1,"external_id":{"isi":["000465169700017"],"pmid":["30819547"]},"intvolume":"       102","publication_status":"published","date_published":"2019-04-17T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"day":"17","date_updated":"2026-06-18T19:03:23Z","year":"2019","type":"journal_article","citation":{"apa":"Stella, F., Baracskay, P., O’Neill, J., &#38; Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">https://doi.org/10.1016/j.neuron.2019.01.052</a>","chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">https://doi.org/10.1016/j.neuron.2019.01.052</a>.","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” <i>Neuron</i>, vol. 102. Elsevier, pp. 450–461, 2019.","ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. <i>Neuron</i>. 2019;102:450-461. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">10.1016/j.neuron.2019.01.052</a>","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.","mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” <i>Neuron</i>, vol. 102, Elsevier, 2019, pp. 450–61, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">10.1016/j.neuron.2019.01.052</a>.","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461."},"title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","volume":102,"project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511"},{"name":"Interneuro plasticity during spatial learning","grant_number":"I 3713-B27","call_identifier":"FWF","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","article_type":"original","abstract":[{"lang":"eng","text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning."}],"ec_funded":1,"page":"450-461","scopus_import":"1","date_created":"2019-04-17T08:28:59Z","_id":"6338","ddc":["570"],"quality_controlled":"1","oa":1,"status":"public","month":"04","publication":"Neuron","isi":1},{"author":[{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.sbi.2019.03.018","oa_version":"None","external_id":{"isi":["000494891800004"]},"issue":"10","publication_status":"published","intvolume":"        58","day":"01","date_updated":"2023-08-25T10:13:31Z","year":"2019","publication_identifier":{"issn":["0959-440X"]},"type":"journal_article","date_published":"2019-10-01T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","citation":{"chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>.","apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">https://doi.org/10.1016/j.sbi.2019.03.018</a>","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. <i>Current Opinion in Structural Biology</i>. 2019;58(10):1-9. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.","ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9.","mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” <i>Current Opinion in Structural Biology</i>, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.03.018\">10.1016/j.sbi.2019.03.018</a>."},"volume":58,"_id":"6343","scopus_import":"1","page":"1-9","date_created":"2019-04-19T11:19:13Z","publisher":"Elsevier","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA."}],"article_type":"original","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","publication":"Current Opinion in Structural Biology","month":"10","status":"public","isi":1,"quality_controlled":"1"},{"quality_controlled":"1","isi":1,"oa":1,"status":"public","publication":"Nature","month":"04","abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2019-04-28T21:59:13Z","page":"378-381","_id":"6348","volume":568,"citation":{"chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>.","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. <i>Nature</i>. 2019;568(7752):378-381. doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” <i>Nature</i>, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., &#38; Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>.","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381."},"title":"Resonant electro-optic frequency comb","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.10608"}],"article_processing_charge":"No","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"date_published":"2019-04-18T00:00:00Z","year":"2019","type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"date_updated":"2025-07-10T11:53:19Z","day":"18","intvolume":"       568","publication_status":"published","issue":"7752","arxiv":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"external_id":{"arxiv":["1808.10608"],"isi":["000464950700053"]},"oa_version":"Preprint","doi":"10.1038/s41586-019-1110-x","author":[{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860"},{"last_name":"Sedlmeir","full_name":"Sedlmeir, Florian","first_name":"Florian"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Schwefel","full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L."}]},{"publication_status":"published","external_id":{"isi":["000470332600049"]},"oa_version":"Published Version","author":[{"first_name":"Andrey Alexandrovich","last_name":"Temnov","full_name":"Temnov, Andrey Alexandrovich"},{"first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich","last_name":"Rogov"},{"last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna","first_name":"Alla Nikolaevna"},{"last_name":"Klychnikova","full_name":"Klychnikova, Elena Valerievna","first_name":"Elena Valerievna"},{"first_name":"Markus","full_name":"Hartl, Markus","last_name":"Hartl"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Charnagalov","full_name":"Charnagalov, Alexej","first_name":"Alexej","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"45bf040bbce1cea274f6013fa18ba21b","relation":"main_file","access_level":"open_access","file_size":1948014,"content_type":"application/pdf","file_id":"6362","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T09:52:36Z","creator":"dernst","file_name":"2019_MolecularBioReport_Temnov.pdf"}],"doi":"10.1007/s11033-019-04765-z","quality_controlled":"1","ddc":["570"],"publication":"Molecular Biology Reports","month":"04","oa":1,"status":"public","corr_author":"1","isi":1,"publisher":"Springer","abstract":[{"lang":"eng","text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10%  O2) and normal (21%  O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different  O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure."}],"acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"_id":"6352","scopus_import":"1","date_created":"2019-04-28T21:59:14Z","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","citation":{"ieee":"A. A. Temnov <i>et al.</i>, “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” <i>Molecular Biology Reports</i>. Springer, 2019.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. 2019. doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., &#38; Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. Springer. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>.","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019)."},"article_processing_charge":"Yes (via OA deal)","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-04-12T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:47:28Z","day":"12","date_updated":"2026-04-16T09:49:11Z","publication_identifier":{"issn":["0301-4851"],"eissn":["1573-4978"]},"year":"2019","type":"journal_article"},{"pmid":1,"external_id":{"pmid":["31000634"],"isi":["000470086100019"]},"oa_version":"Published Version","doi":"10.1104/pp.18.01377","author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"first_name":"Jana","last_name":"Trenner","full_name":"Trenner, Jana"},{"full_name":"Lippmann, Rebecca","last_name":"Lippmann","first_name":"Rebecca"},{"first_name":"Yvonne","full_name":"Poeschl, Yvonne","last_name":"Poeschl"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","full_name":"Zhang, Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Quint","full_name":"Quint, Marcel","first_name":"Marcel"},{"full_name":"Delker, Carolin","last_name":"Delker","first_name":"Carolin"}],"intvolume":"       180","issue":"2","publication_status":"published","volume":180,"title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","citation":{"short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>.","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>.","ieee":"J. Bellstaedt <i>et al.</i>, “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. 2019;180(2):757-766. doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_published":"2019-06-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"type":"journal_article","year":"2019","date_updated":"2026-06-18T19:03:49Z","day":"01","ddc":["580"],"quality_controlled":"1","isi":1,"publication":"Plant Physiology","month":"06","oa":1,"status":"public","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"article_type":"original","publisher":"ASPB","_id":"6366","scopus_import":"1","page":"757-766","date_created":"2019-04-30T15:24:22Z"},{"publication_status":"published","issue":"6","intvolume":"        15","external_id":{"isi":["000468195600018"]},"related_material":{"record":[{"id":"7172","relation":"dissertation_contains","status":"public"}]},"doi":"10.1038/s41589-019-0262-1","author":[{"first_name":"Wim","full_name":"Dejonghe, Wim","last_name":"Dejonghe"},{"last_name":"Sharma","full_name":"Sharma, Isha","first_name":"Isha"},{"first_name":"Bram","full_name":"Denoo, Bram","last_name":"Denoo"},{"first_name":"Steven","full_name":"De Munck, Steven","last_name":"De Munck"},{"last_name":"Lu","full_name":"Lu, Qing","first_name":"Qing"},{"last_name":"Mishev","full_name":"Mishev, Kiril","first_name":"Kiril"},{"first_name":"Haydar","last_name":"Bulut","full_name":"Bulut, Haydar"},{"first_name":"Evelien","full_name":"Mylle, Evelien","last_name":"Mylle"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","full_name":"Vasileva, Mina K","last_name":"Vasileva"},{"last_name":"Savatin","full_name":"Savatin, Daniel V.","first_name":"Daniel V."},{"first_name":"Wim","last_name":"Nerinckx","full_name":"Nerinckx, Wim"},{"first_name":"An","full_name":"Staes, An","last_name":"Staes"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Dominique","full_name":"Audenaert, Dominique","last_name":"Audenaert"},{"last_name":"Yperman","full_name":"Yperman, Klaas","first_name":"Klaas"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"full_name":"Haucke, Volker","last_name":"Haucke","first_name":"Volker"},{"first_name":"Savvas N.","last_name":"Savvides","full_name":"Savvides, Savvas N."},{"first_name":"Johan","full_name":"Winne, Johan","last_name":"Winne"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"oa_version":"None","isi":1,"status":"public","publication":"Nature Chemical Biology","month":"06","quality_controlled":"1","page":"641–649","date_created":"2019-05-05T21:59:11Z","scopus_import":"1","_id":"6377","article_type":"original","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems."}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","volume":15,"citation":{"apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>.","ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. 2019;15(6):641–649. doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>","ieee":"W. Dejonghe <i>et al.</i>, “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” <i>Nature Chemical Biology</i>, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649.","mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>."},"title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","publication_identifier":{"issn":["1552-4450"],"eissn":["1552-4469"]},"type":"journal_article","year":"2019","day":"01","date_updated":"2026-04-08T13:54:44Z","department":[{"_id":"JiFr"}],"date_published":"2019-06-01T00:00:00Z","language":[{"iso":"eng"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","volume":10,"citation":{"short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>","ieee":"H. F. Moussa <i>et al.</i>, “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>."},"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","year":"2019","date_updated":"2026-04-03T09:38:23Z","day":"29","file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"SaSi"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2019-04-29T00:00:00Z","isi":1,"status":"public","oa":1,"publication":"Nature Communications","month":"04","quality_controlled":"1","ddc":["570"],"scopus_import":"1","date_created":"2019-05-13T07:58:35Z","_id":"6412","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates."}],"publisher":"Springer Nature","external_id":{"isi":["000466118700002"]},"doi":"10.1038/s41467-019-09628-6","file":[{"checksum":"6550a328335396c856db4cbdda7d2994","content_type":"application/pdf","file_size":1223647,"file_id":"6448","relation":"main_file","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf","creator":"dernst","date_created":"2019-05-14T08:45:51Z","date_updated":"2020-07-14T12:47:29Z"}],"author":[{"last_name":"Moussa","full_name":"Moussa, Hagar F.","first_name":"Hagar F."},{"last_name":"Bsteh","full_name":"Bsteh, Daniel","first_name":"Daniel"},{"first_name":"Ramesh","last_name":"Yelagandula","full_name":"Yelagandula, Ramesh"},{"full_name":"Pribitzer, Carina","last_name":"Pribitzer","first_name":"Carina"},{"last_name":"Stecher","full_name":"Stecher, Karin","first_name":"Karin"},{"full_name":"Bartalska, Katarina","last_name":"Bartalska","id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"last_name":"Michetti","full_name":"Michetti, Luca","first_name":"Luca"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Jorge A.","last_name":"Zepeda-Martinez","full_name":"Zepeda-Martinez, Jorge A."},{"full_name":"Elling, Ulrich","last_name":"Elling","first_name":"Ulrich"},{"first_name":"Jacob I.","last_name":"Stuckey","full_name":"Stuckey, Jacob I."},{"first_name":"Lindsey I.","last_name":"James","full_name":"James, Lindsey I."},{"first_name":"Stephen V.","last_name":"Frye","full_name":"Frye, Stephen V."},{"last_name":"Bell","full_name":"Bell, Oliver","first_name":"Oliver"}],"oa_version":"Published Version","article_number":"1931","publication_status":"published","issue":"1","intvolume":"        10"},{"year":"2019","type":"journal_article","publication_identifier":{"issn":["0301-9322"]},"day":"01","date_updated":"2026-04-16T09:49:27Z","department":[{"_id":"BjHo"}],"date_published":"2019-08-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1902.07351","open_access":"1"}],"volume":117,"title":"Phase-field simulation of core-annular pipe flow","citation":{"mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>."},"_id":"6413","scopus_import":"1","page":"14-24","date_created":"2019-05-13T07:58:35Z","abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"article_type":"original","publisher":"Elsevier","isi":1,"publication":"International Journal of Multiphase Flow","month":"08","status":"public","oa":1,"quality_controlled":"1","doi":"10.1016/j.ijmultiphaseflow.2019.04.027","author":[{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"last_name":"Plana","full_name":"Plana, Carlos","first_name":"Carlos"},{"last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"oa_version":"Preprint","external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"arxiv":1,"publication_status":"published","intvolume":"       117"},{"doi":"10.1016/j.cois.2019.03.011","type":"journal_article","publication_identifier":{"issn":["2214-5745"],"eissn":["2214-5753"]},"year":"2019","date_updated":"2025-07-10T11:53:22Z","author":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"day":"01","department":[{"_id":"SyCr"}],"oa_version":"None","language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000477666000012"]},"article_processing_charge":"No","volume":33,"title":"Pathogens and disease defense of invasive ants","citation":{"ama":"Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. 2019;33:63-68. doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>.","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68."},"_id":"6415","scopus_import":"1","page":"63-68","date_created":"2019-05-13T07:58:36Z","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"publisher":"Elsevier","publication_status":"published","isi":1,"month":"06","publication":"Current Opinion in Insect Science","status":"public","intvolume":"        33","quality_controlled":"1"},{"intvolume":"        11","issue":"4","publication_status":"published","oa_version":"Published Version","file":[{"file_id":"6446","file_size":1256303,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z","file_name":"2019_GBE_Huylmans.pdf","creator":"dernst"}],"author":[{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","last_name":"Huylmans","full_name":"Huylmans, Ann K"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger","full_name":"Gammerdinger, William J"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"doi":"10.1093/gbe/evz053","related_material":{"record":[{"status":"public","relation":"popular_science","id":"6060"}]},"external_id":{"isi":["000476569800003"]},"publisher":"Oxford University Press","ec_funded":1,"abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"_id":"6418","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2019-05-13T07:58:38Z","page":"1033-1044","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"quality_controlled":"1","month":"04","publication":"Genome biology and evolution","oa":1,"status":"public","isi":1,"date_published":"2019-04-01T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:29Z","day":"01","date_updated":"2025-04-14T07:41:21Z","publication_identifier":{"eissn":["1759-6653"]},"year":"2019","type":"journal_article","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","citation":{"ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044."},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"volume":11,"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"place":"Cham","department":[{"_id":"TaHa"}],"date_published":"2019-03-25T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2523-3041"],"isbn":["9783030041601"],"eisbn":["9783030041618"],"eissn":["2523-305X"]},"type":"book_chapter","year":"2019","day":"25","date_updated":"2025-09-23T11:59:52Z","volume":2,"citation":{"short":"Y. Yang, G. Zhao, in:, 2017 MATRIX Annals, Springer International Publishing, Cham, 2019, pp. 675–691.","ista":"Yang Y, Zhao G. 2019.How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. MATRIX Book Series, vol. 2, 675–691.","mla":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” <i>2017 MATRIX Annals</i>, vol. 2, Springer International Publishing, 2019, pp. 675–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>.","apa":"Yang, Y., &#38; Zhao, G. (2019). How to Sheafify an Elliptic Quantum Group. In <i>2017 MATRIX Annals</i> (Vol. 2, pp. 675–691). Cham: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>","chicago":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” In <i>2017 MATRIX Annals</i>, 2:675–91. MXBS. Cham: Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">https://doi.org/10.1007/978-3-030-04161-8_54</a>.","ama":"Yang Y, Zhao G. How to Sheafify an Elliptic Quantum Group. In: <i>2017 MATRIX Annals</i>. Vol 2. MXBS. Cham: Springer International Publishing; 2019:675-691. doi:<a href=\"https://doi.org/10.1007/978-3-030-04161-8_54\">10.1007/978-3-030-04161-8_54</a>","ieee":"Y. Yang and G. Zhao, “How to Sheafify an Elliptic Quantum Group,” in <i>2017 MATRIX Annals</i>, vol. 2, Cham: Springer International Publishing, 2019, pp. 675–691."},"title":"How to Sheafify an Elliptic Quantum Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1803.06627"}],"abstract":[{"text":"These lecture notes are based on Yang’s talk at the MATRIX program Geometric R-Matrices: from Geometry to Probability, at the University of Melbourne, Dec. 18–22, 2017, and Zhao’s talk at Perimeter Institute for Theoretical Physics in January 2018. We give an introductory survey of the results in Yang and Zhao (Quiver varieties and elliptic quantum groups, 2017. arxiv1708.01418). We discuss a sheafified elliptic quantum group associated to any symmetric Kac-Moody Lie algebra. The sheafification is obtained by applying the equivariant elliptic cohomological theory to the moduli space of representations of a preprojective algebra. By construction, the elliptic quantum group naturally acts on the equivariant elliptic cohomology of Nakajima quiver varieties. As an application, we obtain a relation between the sheafified elliptic quantum group and the global affine Grassmannian over an elliptic curve.","lang":"eng"}],"acknowledgement":"Y.Y. would like to thank the organizers of the MATRIX program Geometric R-Matrices: from Geometry to Probability for their kind invitation, and many participants of the program for useful discussions, including Vassily Gorbounov, Andrei Okounkov, Allen Knutson, Hitoshi Konno, Paul Zinn-Justin. Proposition 1 and Sect. 3.3 are new, for which we thank Hitoshi Konno for interesting discussions and communications. These notes were written when both authors were visiting the Perimeter Institute for Theoretical Physics (PI). We are grateful to PI for the hospitality.","publisher":"Springer International Publishing","date_created":"2025-07-10T13:31:38Z","page":"675-691","_id":"19987","OA_place":"repository","quality_controlled":"1","status":"public","oa":1,"publication":"2017 MATRIX Annals","series_title":"MXBS","month":"03","oa_version":"Preprint","doi":"10.1007/978-3-030-04161-8_54","author":[{"first_name":"Yaping","id":"360D8648-F248-11E8-B48F-1D18A9856A87","last_name":"Yang","full_name":"Yang, Yaping"},{"full_name":"Zhao, Gufang","last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang"}],"external_id":{"arxiv":["1803.06627"]},"arxiv":1,"intvolume":"         2","publication_status":"published","alternative_title":["MATRIX Book Series"]},{"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"date_published":"2019-09-01T00:00:00Z","publication_identifier":{"isbn":["9781786347008"],"eisbn":["9781786347022"]},"type":"book_chapter","year":"2019","date_updated":"2025-09-23T11:53:34Z","day":"01","citation":{"short":"A. De Martino, D. De Martino, E. Marinari, in:, Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471.","mla":"De Martino, A., et al. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” <i>Chemical Kinetics</i>, World Scientific Publishing, 2019, pp. 455–71, doi:<a href=\"https://doi.org/10.1142/9781786347015_0018\">10.1142/9781786347015_0018</a>.","ista":"De Martino A, De Martino D, Marinari E. 2019.The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. , 455–471.","apa":"De Martino, A., De Martino, D., &#38; Marinari, E. (2019). The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In <i>Chemical Kinetics</i> (pp. 455–471). World Scientific Publishing. <a href=\"https://doi.org/10.1142/9781786347015_0018\">https://doi.org/10.1142/9781786347015_0018</a>","ieee":"A. De Martino, D. De Martino, and E. Marinari, “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges,” in <i>Chemical Kinetics</i>, World Scientific Publishing, 2019, pp. 455–471.","ama":"De Martino A, De Martino D, Marinari E. The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: <i>Chemical Kinetics</i>. World Scientific Publishing; 2019:455-471. doi:<a href=\"https://doi.org/10.1142/9781786347015_0018\">10.1142/9781786347015_0018</a>","chicago":"De Martino, A, Daniele De Martino, and E Marinari. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” In <i>Chemical Kinetics</i>, 455–71. World Scientific Publishing, 2019. <a href=\"https://doi.org/10.1142/9781786347015_0018\">https://doi.org/10.1142/9781786347015_0018</a>."},"title":"The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1902.07129","open_access":"1"}],"article_processing_charge":"No","abstract":[{"text":"Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks.","lang":"eng"}],"publisher":"World Scientific Publishing","page":"455-471","date_created":"2025-07-10T13:34:01Z","OA_place":"repository","_id":"19988","quality_controlled":"1","status":"public","oa":1,"publication":"Chemical Kinetics","month":"09","oa_version":"Preprint","doi":"10.1142/9781786347015_0018","author":[{"first_name":"A","last_name":"De Martino","full_name":"De Martino, A"},{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"full_name":"Marinari, E","last_name":"Marinari","first_name":"E"}],"external_id":{"arxiv":["1902.07129"]},"arxiv":1,"publication_status":"published"},{"title":"Aktionspotenzial: Fortleitung im Axon","citation":{"apa":"Jonas, P. M. (2019). Aktionspotenzial: Fortleitung im Axon. In <i>Physiologie des Menschen</i> (32nd ed., pp. 72–82). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">https://doi.org/10.1007/978-3-662-56468-4_7</a>","ama":"Jonas PM. Aktionspotenzial: Fortleitung im Axon. In: <i>Physiologie des Menschen</i>. 32nd ed. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature; 2019:72-82. doi:<a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">10.1007/978-3-662-56468-4_7</a>","ieee":"P. M. Jonas, “Aktionspotenzial: Fortleitung im Axon,” in <i>Physiologie des Menschen</i>, 32nd ed., Berlin, Heidelberg: Springer Nature, 2019, pp. 72–82.","chicago":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” In <i>Physiologie des Menschen</i>, 32nd ed., 72–82. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">https://doi.org/10.1007/978-3-662-56468-4_7</a>.","mla":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” <i>Physiologie des Menschen</i>, 32nd ed., Springer Nature, 2019, pp. 72–82, doi:<a href=\"https://doi.org/10.1007/978-3-662-56468-4_7\">10.1007/978-3-662-56468-4_7</a>.","ista":"Jonas PM. 2019.Aktionspotenzial: Fortleitung im Axon. In: Physiologie des Menschen. , 72–82.","short":"P.M. Jonas, in:, Physiologie des Menschen, 32nd ed., Springer Nature, Berlin, Heidelberg, 2019, pp. 72–82."},"article_processing_charge":"No","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","language":[{"iso":"ger"}],"date_published":"2019-04-02T00:00:00Z","department":[{"_id":"PeJo"}],"place":"Berlin, Heidelberg","date_updated":"2025-09-23T11:44:57Z","day":"02","author":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"doi":"10.1007/978-3-662-56468-4_7","year":"2019","publication_identifier":{"issn":["0937-7433"],"isbn":["9783662564677"],"eissn":["2512-5214"],"eisbn":["9783662564684"]},"type":"book_chapter","quality_controlled":"1","series_title":"Springer-Lehrbuch","month":"04","publication":"Physiologie des Menschen","status":"public","corr_author":"1","publication_status":"published","publisher":"Springer Nature","edition":"32","abstract":[{"text":"Neurone empfangen Eingangssignale, konvertieren diese in Aktionspotenziale und generieren schließlich Ausgangssignale auf ihren Zielzellen. Dabei sind die zu überwindenden räumlichen Distanzen oft groß. Daher ist entscheidend, dass elektrische Signale in Nervenzellen schnell von einem zum anderen Ort geleitet werden können. Diese wichtige Aufgabe erfüllt das Axon, der „Ausgangsfortsatz“ der Nervenzelle. Für die schnelle Leitung des Aktionspotenzials sind sowohl die passiven Eigenschaften des axonalen Kabels als auch die aktiven Eigenschaften der Zellmembran von entscheidender Bedeutung. Die Evolution bedient sich zweier Tricks, um die Leitungsgeschwindigkeit des Aktionspotenzials zu maximieren. Der eine Trick ist die Zunahme des Axondurchmessers. Der andere Trick ist die Ausbildung von Markscheiden. Dies führt bei nahezu gleichem Platzbedarf zu einer Zunahme der Leistungsgeschwindigkeit um fast zwei Größenordnungen. Die Aktionspotenzialleitung an myelinisierten Axonen erfolgt „saltatorisch“.","lang":"ger"}],"_id":"19989","date_created":"2025-07-10T13:36:36Z","page":"72-82"},{"publisher":"ACM","abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","scopus_import":"1","date_created":"2021-10-27T14:57:06Z","_id":"10190","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_place":"publisher","keyword":["safety","risk","reliability and quality","software"],"ddc":["000"],"quality_controlled":"1","oa":1,"status":"public","month":"10","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","corr_author":"1","language":[{"iso":"eng"}],"date_published":"2019-10-10T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"has_accepted_license":"1","day":"10","date_updated":"2026-04-08T07:00:31Z","file_date_updated":"2021-11-12T11:41:56Z","publication_identifier":{"eissn":["2475-1421"]},"year":"2019","type":"conference","citation":{"short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic partial order reduction. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>.","ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens, Greece, 2019, vol. 3."},"title":"Value-centric dynamic partial order reduction","volume":3,"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"conference":{"start_date":"2019-10-23","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","end_date":"2019-10-25","location":"Athens, Greece"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","arxiv":1,"intvolume":"         3","publication_status":"published","article_number":"124","oa_version":"Published Version","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"last_name":"Toman","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"2019_ACM_Chatterjee.pdf","creator":"cchlebak","date_created":"2021-11-12T11:41:56Z","success":1,"date_updated":"2021-11-12T11:41:56Z","checksum":"2149979c46964c4d117af06ccb6c0834","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10278","file_size":570829}],"doi":"10.1145/3360550","related_material":{"record":[{"id":"10199","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["1909.00989"]}},{"department":[{"_id":"GaNo"}],"date_published":"2019-01-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","year":"2019","date_updated":"2026-06-18T08:42:55Z","day":"01","volume":27,"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","citation":{"ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” <i>European Journal of Human Genetics</i>, vol. 27. Springer Nature, pp. 161–166, 2019.","apa":"Marsh, A., Novarino, G., Lockhart, P., &#38; Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. 2019;27:161-166. doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>.","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>, vol. 27, Springer Nature, 2019, pp. 161–66, doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"article_processing_charge":"No","acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","article_type":"original","abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"publisher":"Springer Nature","publist_id":"7949","_id":"105","date_created":"2018-12-11T11:44:39Z","scopus_import":"1","page":"161-166","ddc":["570"],"quality_controlled":"1","isi":1,"month":"01","publication":"European Journal of Human Genetics","status":"public","oa":1,"oa_version":"Published Version","doi":"10.1038/s41431-018-0231-2","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia"},{"first_name":"Paul","last_name":"Lockhart","full_name":"Lockhart, Paul"},{"first_name":"Richard","last_name":"Leventer","full_name":"Leventer, Richard"}],"pmid":1,"external_id":{"pmid":["30089829"],"isi":["000454111500019"]},"intvolume":"        27","publication_status":"published"},{"intvolume":"        61","publication_status":"published","oa_version":"Published Version","doi":"10.29007/m75b","file":[{"file_name":"2019_ARCH19_Immler.pdf","creator":"dernst","date_created":"2020-03-24T07:36:36Z","date_updated":"2020-07-14T12:48:00Z","checksum":"9138977a06fcd6a95976eb4bca875f0c","file_size":1934830,"file_id":"7617","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"author":[{"first_name":"Fabian","last_name":"Immler","full_name":"Immler, Fabian"},{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"},{"full_name":"Benet, Luis","last_name":"Benet","first_name":"Luis"},{"first_name":"Alexandre","full_name":"Chapoutot, Alexandre","last_name":"Chapoutot"},{"first_name":"Xin","full_name":"Chen, Xin","last_name":"Chen"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"first_name":"Luca","full_name":"Geretti, Luca","last_name":"Geretti"},{"first_name":"Niklas","full_name":"Kochdumper, Niklas","last_name":"Kochdumper"},{"first_name":"David P.","last_name":"Sanders","full_name":"Sanders, David P."},{"last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"quality_controlled":"1","corr_author":"1","publication":"EPiC Series in Computing","month":"05","oa":1,"status":"public","abstract":[{"text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.","lang":"eng"}],"publisher":"EasyChair","_id":"7576","date_created":"2020-03-08T23:00:49Z","scopus_import":"1","page":"41-61","volume":61,"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","citation":{"ieee":"F. Immler <i>et al.</i>, “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, Montreal, Canada, 2019, vol. 61, pp. 41–61.","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 61. EasyChair; 2019:41-61. doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 61:41–61. EasyChair, 2019. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>.","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 61, EasyChair, 2019, pp. 41–61, doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>.","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair, 2019, pp. 41–61."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","conference":{"start_date":"2019-04-15","location":"Montreal, Canada","end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"has_accepted_license":"1","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"date_published":"2019-05-25T00:00:00Z","publication_identifier":{"eissn":["2398-7340"]},"year":"2019","type":"conference","file_date_updated":"2020-07-14T12:48:00Z","day":"25","date_updated":"2026-04-03T09:51:13Z"},{"oa_version":"Preprint","doi":"10.1109/ITW44776.2019.8989292","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]},"external_id":{"isi":["000540384500015"],"arxiv":["1812.01475"]},"arxiv":1,"publication_status":"published","article_number":"8989292","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"date_published":"2019-08-01T00:00:00Z","year":"2019","type":"conference","publication_identifier":{"isbn":["9781538669006"]},"day":"01","date_updated":"2026-04-07T12:59:24Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"A tight upper bound on mutual information","citation":{"short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” <i>IEEE Information Theory Workshop, ITW 2019</i>, 8989292, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>.","apa":"Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2019). A tight upper bound on mutual information. In <i>IEEE Information Theory Workshop, ITW 2019</i>. Visby, Sweden: IEEE. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>.","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in <i>IEEE Information Theory Workshop, ITW 2019</i>, Visby, Sweden, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"conference":{"start_date":"2019-08-25","name":"Information Theory Workshop","end_date":"2019-08-28","location":"Visby, Sweden"},"ec_funded":1,"abstract":[{"lang":"eng","text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound."}],"publisher":"IEEE","_id":"7606","scopus_import":"1","date_created":"2020-03-22T23:00:47Z","quality_controlled":"1","isi":1,"publication":"IEEE Information Theory Workshop, ITW 2019","month":"08","oa":1,"status":"public"},{"quality_controlled":"1","status":"public","publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","month":"10","article_number":"748-752","publication_status":"published","isi":1,"publisher":"IEEE","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN."}],"date_created":"2020-04-05T22:00:50Z","scopus_import":"1","_id":"7639","citation":{"chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>.","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., &#38; Blaschko, M. B. (2019). Function norms for neural networks. In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. Seoul, South Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>","ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>","ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, Seoul, South Korea, 2019.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, 748–752, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>.","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019."},"title":"Function norms for neural networks","conference":{"start_date":"2019-10-27","location":"Seoul, South Korea","name":"ICCVW: International Conference on Computer Vision Workshop","end_date":"2019-10-28"},"article_processing_charge":"No","external_id":{"isi":["000554591600090"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_published":"2019-10-01T00:00:00Z","oa_version":"None","department":[{"_id":"VlKo"}],"day":"01","date_updated":"2023-09-08T11:19:12Z","author":[{"first_name":"Amal","last_name":"Rannen-Triki","full_name":"Rannen-Triki, Amal"},{"first_name":"Maxim","full_name":"Berman, Maxim","last_name":"Berman"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"full_name":"Blaschko, Matthew B.","last_name":"Blaschko","first_name":"Matthew B."}],"year":"2019","type":"conference","publication_identifier":{"isbn":["9781728150239"]},"doi":"10.1109/ICCVW.2019.00097"}]