[{"volume":114,"article_processing_charge":"No","arxiv":1,"oa_version":"Submitted Version","month":"02","citation":{"ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” <i>Biophysical Journal</i>, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","apa":"Dasbiswas, K., Hannezo, E. B., &#38; Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. 2018;114(4):968-977. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>.","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>. Biophysical Society, 2018. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>."},"day":"27","publication_status":"published","status":"public","doi":"10.1016/j.bpj.2017.12.022","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"issue":"4","_id":"421","title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","author":[{"first_name":"Kinjal","full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Claude-Edouard B","first_name":"Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Biophysical Society","intvolume":"       114","main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"date_created":"2018-12-11T11:46:23Z","scopus_import":"1","date_published":"2018-02-27T00:00:00Z","external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"publist_id":"7403","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"EdHa"}],"page":"968 - 977","date_updated":"2023-09-19T10:13:55Z","publication":"Biophysical Journal","year":"2018","oa":1},{"intvolume":"       100","publisher":"Springer","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7401","date_published":"2018-01-01T00:00:00Z","external_id":{"isi":["000433113900004"]},"scopus_import":"1","date_created":"2018-12-11T11:46:23Z","publication":"Flow Turbulence and Combustion","date_updated":"2024-03-25T23:30:20Z","related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"page":"919 - 942","oa":1,"year":"2018","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2018_FlowTurbulenceCombust_Kuehnen.pdf","file_size":2210020,"relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:46:25Z","access_level":"open_access","content_type":"application/pdf","checksum":"d7c0bade150faabca150b0a9986e60ca","file_id":"5717","date_created":"2018-12-17T15:52:37Z"}],"has_accepted_license":"1","volume":100,"article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"ama":"Kühnen J, Scarselli D, Schaner M, Hof B. Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. 2018;100(4):919-942. doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>","short":"J. Kühnen, D. Scarselli, M. Schaner, B. Hof, Flow Turbulence and Combustion 100 (2018) 919–942.","ista":"Kühnen J, Scarselli D, Schaner M, Hof B. 2018. Relaminarization by steady modification of the streamwise velocity profile in a pipe. Flow Turbulence and Combustion. 100(4), 919–942.","apa":"Kühnen, J., Scarselli, D., Schaner, M., &#38; Hof, B. (2018). Relaminarization by steady modification of the streamwise velocity profile in a pipe. <i>Flow Turbulence and Combustion</i>. Springer. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>","ieee":"J. Kühnen, D. Scarselli, M. Schaner, and B. Hof, “Relaminarization by steady modification of the streamwise velocity profile in a pipe,” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4. Springer, pp. 919–942, 2018.","mla":"Kühnen, Jakob, et al. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>, vol. 100, no. 4, Springer, 2018, pp. 919–42, doi:<a href=\"https://doi.org/10.1007/s10494-018-9896-4\">10.1007/s10494-018-9896-4</a>.","chicago":"Kühnen, Jakob, Davide Scarselli, Markus Schaner, and Björn Hof. “Relaminarization by Steady Modification of the Streamwise Velocity Profile in a Pipe.” <i>Flow Turbulence and Combustion</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10494-018-9896-4\">https://doi.org/10.1007/s10494-018-9896-4</a>."},"month":"01","ddc":["530"],"file_date_updated":"2020-07-14T12:46:25Z","oa_version":"Published Version","project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"publication_status":"published","status":"public","ec_funded":1,"author":[{"full_name":"Kühnen, Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","orcid":"0000-0003-4312-0179"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","full_name":"Scarselli, Davide","last_name":"Scarselli","orcid":"0000-0001-5227-4271"},{"id":"316CE034-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Schaner, Markus","last_name":"Schaner"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof"}],"title":"Relaminarization by steady modification of the streamwise velocity profile in a pipe","_id":"422","issue":"4","abstract":[{"lang":"eng","text":"We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device which injects fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the skin friction in the far downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant local skin friction drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle."}],"doi":"10.1007/s10494-018-9896-4"},{"publisher":"eLife Sciences Publications","intvolume":"         7","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7400","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_created":"2018-12-11T11:46:23Z","scopus_import":"1","external_id":{"isi":["000431035800001"]},"date_published":"2018-03-09T00:00:00Z","date_updated":"2023-09-11T12:49:17Z","publication":"eLife","article_number":"e32035","related_material":{"record":[{"status":"public","relation":"research_data","id":"9840"}]},"oa":1,"year":"2018","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":3533881,"file_name":"2018_eLife_Payne.pdf","content_type":"application/pdf","checksum":"447cf6e680bdc3c01062a8737d876569","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T10:36:07Z","file_id":"5689"}],"article_processing_charge":"No","volume":7,"has_accepted_license":"1","ddc":["576"],"month":"03","file_date_updated":"2020-07-14T12:46:25Z","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>"},"day":"09","oa_version":"Published Version","project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","_id":"423","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","author":[{"first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612"}],"doi":"10.7554/eLife.32035","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}]},{"oa":1,"year":"2018","date_updated":"2023-09-11T13:38:49Z","publication":"Journal of the ACM","article_number":"5","article_type":"original","related_material":{"record":[{"id":"2157","status":"public","relation":"earlier_version"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7398","department":[{"_id":"UlWa"}],"date_created":"2018-12-11T11:46:24Z","scopus_import":"1","external_id":{"isi":["000425685900006"],"arxiv":["1402.0815"]},"date_published":"2018-01-01T00:00:00Z","publisher":"ACM","intvolume":"        65","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"_id":"425","title":"Embeddability in the 3-Sphere is decidable","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"first_name":"Eric","full_name":"Sedgwick, Eric","last_name":"Sedgwick"},{"orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Tancer, Martin","last_name":"Tancer"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner"}],"doi":"10.1145/3078632","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"issue":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"status":"public","publication_status":"published","month":"01","citation":{"apa":"Matoušek, J., Sedgwick, E., Tancer, M., &#38; Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” <i>Journal of the ACM</i>, vol. 65, no. 1. ACM, 2018.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. 2018;65(1). doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>, vol. 65, no. 1, 5, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>."},"day":"01","oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":65},{"article_processing_charge":"No","volume":107,"month":"05","day":"01","citation":{"chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>.","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>, vol. 107, Elsevier, 2018, pp. 284–90, doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. 2018;107:284-290. doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>","ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” <i>Journal of Insect Physiology</i>, vol. 107. Elsevier, pp. 284–290, 2018.","apa":"Metzler, S., Schrempf, A., &#38; Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>"},"oa_version":"None","status":"public","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","publication_status":"published","_id":"426","author":[{"orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina"},{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"}],"title":"Individual- and ejaculate-specific sperm traits in ant males","doi":"10.1016/j.jinsphys.2017.12.003","abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"intvolume":"       107","publisher":"Elsevier","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publist_id":"7397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"SyCr"}],"scopus_import":"1","date_created":"2018-12-11T11:46:25Z","date_published":"2018-05-01T00:00:00Z","external_id":{"isi":["000434751100034"]},"date_updated":"2023-09-12T07:43:26Z","publication":"Journal of Insect Physiology","page":"284-290","year":"2018"},{"article_processing_charge":"No","volume":97,"arxiv":1,"oa_version":"Preprint","month":"02","citation":{"short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos,  Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions.  Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510.","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2018;97(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">10.1103/PhysRevA.97.022510</a>","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., &#38; Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">https://doi.org/10.1103/PhysRevA.97.022510</a>","ieee":"P. Amaro <i>et al.</i>, “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 2. American Physical Society, 2018.","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">https://doi.org/10.1103/PhysRevA.97.022510</a>.","mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.022510\">10.1103/PhysRevA.97.022510</a>."},"day":"21","ec_funded":1,"acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","status":"public","publication_status":"published","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevA.97.022510","abstract":[{"lang":"eng","text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements."}],"issue":"2","_id":"427","title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"last_name":"Loureiro","full_name":"Loureiro, Ulisses","first_name":"Ulisses"},{"last_name":"Safari","full_name":"Safari, Laleh","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"full_name":"Stöhlker, Thomas","last_name":"Stöhlker","first_name":"Thomas"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"American Physical Society","intvolume":"        97","main_file_link":[{"url":"https://arxiv.org/abs/1802.07920","open_access":"1"}],"date_created":"2018-12-11T11:46:25Z","scopus_import":"1","date_published":"2018-02-21T00:00:00Z","external_id":{"arxiv":["1802.07920"],"isi":["000425601000004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7396","department":[{"_id":"MiLe"}],"article_number":"022510","article_type":"original","date_updated":"2023-09-15T12:09:35Z","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","year":"2018","oa":1},{"file":[{"file_name":"2018_PNAS_Salanenka.pdf","relation":"main_file","creator":"dernst","file_size":1924101,"access_level":"open_access","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","content_type":"application/pdf","date_updated":"2020-07-14T12:46:26Z","file_id":"5700","date_created":"2018-12-17T12:30:14Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"No","volume":115,"has_accepted_license":"1","month":"04","file_date_updated":"2020-07-14T12:46:26Z","ddc":["580"],"day":"03","citation":{"chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>.","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>PNAS</i>, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>PNAS</i>. 2018;115(14):3716-3721. doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>","ieee":"Y. Salanenka <i>et al.</i>, “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” <i>PNAS</i>, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., &#38; Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>"},"oa_version":"Published Version","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"ec_funded":1,"acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","publication_status":"published","status":"public","_id":"428","author":[{"last_name":"Salanenka","full_name":"Salanenka, Yuliya","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"full_name":"Tabata, Kaori","last_name":"Tabata","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","first_name":"Kaori"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Glanc, Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"}],"title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","doi":"10.1073/pnas.1721760115","issue":"14","abstract":[{"lang":"eng","text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses."}],"intvolume":"       115","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7395","department":[{"_id":"JiFr"}],"scopus_import":"1","date_created":"2018-12-11T11:46:25Z","date_published":"2018-04-03T00:00:00Z","external_id":{"isi":["000429012500073"]},"date_updated":"2025-05-07T11:12:27Z","publication":"PNAS","page":" 3716 - 3721","oa":1,"year":"2018"},{"file":[{"file_name":"2018_PNAS_Rybicki.pdf","creator":"dernst","file_size":4070777,"relation":"main_file","date_updated":"2020-07-14T12:46:26Z","access_level":"open_access","checksum":"df7ac544a587c06b75692653b9fabd18","content_type":"application/pdf","file_id":"6258","date_created":"2019-04-09T08:02:50Z"}],"article_processing_charge":"No","volume":115,"has_accepted_license":"1","month":"10","ddc":["570","577"],"file_date_updated":"2020-07-14T12:46:26Z","day":"02","citation":{"ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>PNAS</i>. 2018;115(42):10690-10695. doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” <i>PNAS</i>, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","apa":"Rybicki, J., Kisdi, E., &#38; Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>.","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>PNAS</i>, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>."},"pubrep_id":"1063","oa_version":"Submitted Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","status":"public","publication_status":"published","_id":"43","author":[{"orcid":"0000-0002-6432-6646","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","full_name":"Rybicki, Joel"},{"last_name":"Kisdi","full_name":"Kisdi, Eva","first_name":"Eva"},{"full_name":"Anttila, Jani","last_name":"Anttila","first_name":"Jani"}],"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","doi":"10.1073/pnas.1721061115","issue":"42","abstract":[{"text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.","lang":"eng"}],"intvolume":"       115","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8011","department":[{"_id":"DaAl"}],"scopus_import":"1","date_created":"2018-12-11T11:44:19Z","external_id":{"isi":["000447491300057"]},"date_published":"2018-10-02T00:00:00Z","date_updated":"2023-09-13T08:57:38Z","publication":"PNAS","page":"10690 - 10695","oa":1,"year":"2018"},{"day":"01","pubrep_id":"1012","citation":{"ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” <i>Genetics</i>, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","apa":"Novembre, J., &#38; Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. 2018;208(4):1351-1355. doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>."},"month":"04","file_date_updated":"2020-07-14T12:46:26Z","ddc":["576"],"oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:40Z","file_id":"4958","creator":"system","file_size":500129,"relation":"main_file","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","checksum":"3d838dc285df394376555b794b6a5ad1","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:26Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":208,"article_processing_charge":"No","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Tread lightly interpreting polygenic tests of selection","_id":"430","issue":"4","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"doi":"10.1534/genetics.118.300786","publication_status":"published","status":"public","department":[{"_id":"NiBa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7393","date_published":"2018-04-01T00:00:00Z","external_id":{"isi":["000429094400005"]},"scopus_import":"1","date_created":"2018-12-11T11:46:26Z","intvolume":"       208","publisher":"Genetics Society of America","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2018","publication":"Genetics","date_updated":"2023-09-19T10:17:30Z","page":"1351 - 1355"},{"publisher":"Springer","intvolume":"     10692","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7390","external_id":{"arxiv":["1708.08037"]},"date_published":"2018-01-21T00:00:00Z","date_created":"2018-12-11T11:46:27Z","scopus_import":1,"date_updated":"2023-08-24T14:39:32Z","related_material":{"record":[{"id":"5857","status":"public","relation":"later_version"}]},"page":"160 - 166","oa":1,"year":"2018","alternative_title":["LNCS"],"arxiv":1,"volume":10692,"citation":{"mla":"Fulek, Radoslav, and János Pach. <i>Thrackles: An Improved Upper Bound</i>. Vol. 10692, Springer, 2018, pp. 160–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>.","apa":"Fulek, R., &#38; Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166."},"day":"21","month":"01","oa_version":"Submitted Version","conference":{"end_date":"2017-09-27","location":"Boston, MA, United States","start_date":"201-09-25","name":"GD 2017: Graph Drawing and Network Visualization"},"publication_status":"published","status":"public","title":"Thrackles: An improved upper bound","author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"János","last_name":"Pach","full_name":"Pach, János"}],"_id":"433","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"doi":"10.1007/978-3-319-73915-1_14"},{"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"IEEE","intvolume":"        19","date_created":"2018-12-11T11:46:27Z","scopus_import":"1","external_id":{"isi":["000446651100020"]},"date_published":"2018-01-01T00:00:00Z","publist_id":"7389","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"page":"3320 - 3333","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1205"}]},"date_updated":"2023-09-18T08:12:49Z","publication":"IEEE Transactions on Intelligent Transportation Systems","year":"2018","article_processing_charge":"No","volume":19,"oa_version":"None","month":"01","citation":{"ieee":"Y. Jiang <i>et al.</i>, “Safety-assured model-driven design of the multifunction vehicle bus controller,” <i>IEEE Transactions on Intelligent Transportation Systems</i>, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., &#38; Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. <i>IEEE Transactions on Intelligent Transportation Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TITS.2017.2778077\">https://doi.org/10.1109/TITS.2017.2778077</a>","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. <i>IEEE Transactions on Intelligent Transportation Systems</i>. 2018;19(10):3320-3333. doi:<a href=\"https://doi.org/10.1109/TITS.2017.2778077\">10.1109/TITS.2017.2778077</a>","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” <i>IEEE Transactions on Intelligent Transportation Systems</i>, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:<a href=\"https://doi.org/10.1109/TITS.2017.2778077\">10.1109/TITS.2017.2778077</a>.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” <i>IEEE Transactions on Intelligent Transportation Systems</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TITS.2017.2778077\">https://doi.org/10.1109/TITS.2017.2778077</a>."},"day":"01","status":"public","publication_status":"published","doi":"10.1109/TITS.2017.2778077","abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"issue":"10","_id":"434","title":"Safety-assured model-driven design of the multifunction vehicle bus controller","author":[{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"first_name":"Han","last_name":"Liu","full_name":"Liu, Han"},{"first_name":"Huobing","full_name":"Song, Huobing","last_name":"Song"},{"last_name":"Kong","full_name":"Kong, Hui","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941"},{"last_name":"Wang","full_name":"Wang, Rui","first_name":"Rui"},{"last_name":"Guan","full_name":"Guan, Yong","first_name":"Yong"},{"first_name":"Lui","last_name":"Sha","full_name":"Sha, Lui"}]},{"issue":"3","abstract":[{"lang":"eng","text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum."}],"doi":"10.1364/OL.43.000607","author":[{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","full_name":"Midya, Bikashkali"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"title":"Coherent-perfect-absorber and laser for bound states in a continuum","_id":"435","status":"public","publication_status":"published","acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa_version":"Preprint","day":"01","citation":{"ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” <i>Optics Letters</i>, vol. 43, no. 3. Optica  Publishing Group, pp. 607–610, 2018.","apa":"Midya, B., &#38; Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. Optica  Publishing Group. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. 2018;43(3):607-610. doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>, vol. 43, no. 3, Optica  Publishing Group, 2018, pp. 607–10, doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>. Optica  Publishing Group, 2018. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>."},"month":"02","volume":43,"article_processing_charge":"No","arxiv":1,"year":"2018","oa":1,"page":"607 - 610","publication":"Optics Letters","date_updated":"2023-10-17T12:15:06Z","external_id":{"isi":["000423776600066"],"arxiv":["1711.01986"]},"date_published":"2018-02-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:46:27Z","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7388","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"        43","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.01986"}],"publisher":"Optica  Publishing Group"},{"article_number":"060601 ","related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2023-09-13T08:52:27Z","publication":"Physical Review Letters","year":"2018","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"       120","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"publisher":"American Physical Society","scopus_import":"1","date_created":"2018-12-11T11:46:28Z","date_published":"2018-02-07T00:00:00Z","external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"publist_id":"7387","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JoFi"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevLett.120.060601","issue":"6","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"_id":"436","author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"last_name":"Aquilina","full_name":"Aquilina, Matteo","first_name":"Matteo"},{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"}],"title":"Manipulating the flow of thermal noise in quantum devices","volume":120,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"02","day":"07","citation":{"mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” <i>Physical Review Letters</i>, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">10.1103/PhysRevLett.120.060601</a>.","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">https://doi.org/10.1103/PhysRevLett.120.060601</a>.","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. <i>Physical Review Letters</i>. 2018;120(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">10.1103/PhysRevLett.120.060601</a>","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","apa":"Barzanjeh, S., Aquilina, M., &#38; Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.120.060601\">https://doi.org/10.1103/PhysRevLett.120.060601</a>","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” <i>Physical Review Letters</i>, vol. 120, no. 6. American Physical Society, 2018."}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7386","department":[{"_id":"MiSi"},{"_id":"Bio"}],"acknowledged_ssus":[{"_id":"SSU"}],"scopus_import":"1","date_created":"2018-12-11T11:46:28Z","external_id":{"isi":["000434963700016"]},"date_published":"2018-02-13T00:00:00Z","intvolume":"        48","publisher":"Wiley-Blackwell","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"oa":1,"year":"2018","date_updated":"2023-09-11T14:01:18Z","publication":"European Journal of Immunology","page":"1074 - 1077","ddc":["570"],"month":"02","file_date_updated":"2020-07-14T12:46:27Z","day":"13","citation":{"ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” <i>European Journal of Immunology</i>, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., &#38; Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. <i>European Journal of Immunology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/eji.201747358\">https://doi.org/10.1002/eji.201747358</a>","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. <i>European Journal of Immunology</i>. 2018;48(6):1074-1077. doi:<a href=\"https://doi.org/10.1002/eji.201747358\">10.1002/eji.201747358</a>","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” <i>European Journal of Immunology</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1002/eji.201747358\">https://doi.org/10.1002/eji.201747358</a>.","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” <i>European Journal of Immunology</i>, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:<a href=\"https://doi.org/10.1002/eji.201747358\">10.1002/eji.201747358</a>."},"pubrep_id":"1067","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:13:56Z","file_id":"5044","content_type":"application/pdf","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","access_level":"open_access","date_updated":"2020-07-14T12:46:27Z","creator":"system","file_size":590106,"relation":"main_file","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"Yes (via OA deal)","volume":48,"has_accepted_license":"1","_id":"437","author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X"},{"orcid":"0000-0003-2856-3369","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"last_name":"Haecker","full_name":"Haecker, Hans","first_name":"Hans"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","doi":"10.1002/eji.201747358","issue":"6","abstract":[{"text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.","lang":"eng"}],"project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"ec_funded":1,"status":"public","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the  scientific  support units at IST Austria for excellent technical support.   ","publication_status":"published"},{"_id":"438","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Alexandra","last_name":"Vandervelde","full_name":"Vandervelde, Alexandra"},{"full_name":"Albanese, Tanino","last_name":"Albanese","first_name":"Tanino"},{"first_name":"Lendert","last_name":"Gelens","full_name":"Gelens, Lendert"},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}],"doi":"10.1093/nar/gky079","abstract":[{"lang":"eng","text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress."}],"issue":"6","project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"publication_status":"published","status":"public","month":"04","ddc":["576"],"file_date_updated":"2020-07-14T12:46:27Z","citation":{"chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” <i>Nucleic Acids Research</i>, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. 2018;46(6):2918-2931. doi:<a href=\"https://doi.org/10.1093/nar/gky079\">10.1093/nar/gky079</a>","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., &#38; Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gky079\">https://doi.org/10.1093/nar/gky079</a>","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” <i>Nucleic Acids Research</i>, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018."},"pubrep_id":"971","day":"06","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"system","file_size":5027978,"relation":"main_file","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","checksum":"3ff4f545c27e11a4cd20ccb30778793e","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:27Z","date_created":"2018-12-12T10:15:30Z","file_id":"5151"}],"article_processing_charge":"Yes (in subscription journal)","volume":46,"has_accepted_license":"1","oa":1,"year":"2018","date_updated":"2024-02-21T13:44:45Z","publication":"Nucleic Acids Research","page":"2918-2931","related_material":{"record":[{"id":"5569","relation":"popular_science","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaGu"}],"date_created":"2018-12-11T11:46:29Z","scopus_import":"1","external_id":{"isi":["000429009500021"]},"date_published":"2018-04-06T00:00:00Z","publisher":"Oxford University Press","intvolume":"        46","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1},{"publisher":"American Physical Society","intvolume":"        98","main_file_link":[{"url":"https://arxiv.org/abs/1806.10933","open_access":"1"}],"isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"publist_id":"8010","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000447919100001"],"arxiv":["1806.10933"]},"date_published":"2018-10-22T00:00:00Z","date_created":"2018-12-11T11:44:19Z","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","publication":"Physical Review B","date_updated":"2023-10-10T13:28:49Z","article_number":"155134","oa":1,"year":"2018","arxiv":1,"article_processing_charge":"No","volume":98,"citation":{"ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. 2018;98(15). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>","ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” <i>Physical Review B</i>, vol. 98, no. 15. American Physical Society, 2018.","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., &#38; Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>.","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>."},"day":"22","month":"10","oa_version":"Preprint","publication_status":"published","status":"public","title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","author":[{"last_name":"Turner","full_name":"Turner, C J","first_name":"C J"},{"last_name":"Michailidis","full_name":"Michailidis, Alexios","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064"},{"full_name":"Abanin, D A","last_name":"Abanin","first_name":"D A"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"last_name":"Papić","full_name":"Papić, Z","first_name":"Z"}],"_id":"44","abstract":[{"text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization.","lang":"eng"}],"issue":"15","doi":"10.1103/PhysRevB.98.155134"},{"file_date_updated":"2020-07-14T12:46:29Z","month":"01","ddc":["576","581"],"day":"05","citation":{"apa":"Li, L., Krens, G., Fendrych, M., &#38; Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-Protocol</i>. Bio-protocol. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” <i>Bio-protocol</i>, vol. 8, no. 1. Bio-protocol, 2018.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-protocol</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>. Bio-protocol, 2018. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>.","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>, vol. 8, no. 1, Bio-protocol, 2018, doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>."},"pubrep_id":"970","oa_version":"Published Version","file":[{"checksum":"6644ba698206eda32b0abf09128e63e3","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:29Z","relation":"main_file","file_size":11352389,"creator":"system","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","date_created":"2018-12-12T10:17:43Z","file_id":"5299"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":8,"article_processing_charge":"No","has_accepted_license":"1","_id":"442","author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Krens, Gabriel","last_name":"Krens"},{"orcid":"0000-0002-9767-8699","last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","doi":"10.21769/BioProtoc.2685","issue":"1","abstract":[{"text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.","lang":"eng"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["2331-8325"]},"ec_funded":1,"acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","publication_status":"published","status":"public","publist_id":"7381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"Bio"}],"date_created":"2018-12-11T11:46:30Z","date_published":"2018-01-05T00:00:00Z","intvolume":"         8","publisher":"Bio-protocol","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2018","date_updated":"2024-10-29T10:22:43Z","publication":"Bio-protocol","article_type":"original","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]}},{"publication":"Communications on Pure and Applied Mathematics","date_updated":"2023-09-19T10:09:40Z","article_type":"original","page":"577 - 614","oa":1,"year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"intvolume":"        71","publisher":"Wiley-Blackwell","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"RoSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7377","date_published":"2018-03-01T00:00:00Z","external_id":{"arxiv":["1606.07355"],"isi":["000422675800004"]},"date_created":"2018-12-11T11:46:31Z","publication_status":"published","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","status":"public","author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan Thanh","full_name":"Phan Thanh, Nam"},{"full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch","first_name":"Hanne"}],"title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","_id":"446","issue":"3","abstract":[{"lang":"eng","text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z &gt; 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential."}],"doi":"10.1002/cpa.21717","arxiv":1,"volume":71,"article_processing_charge":"No","day":"01","citation":{"ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. 2018;71(3):577-614. doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","apa":"Frank, R., Nam, P., &#38; Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>."},"month":"03","oa_version":"Preprint"},{"department":[{"_id":"BeVi"}],"publist_id":"7375","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000426559600026"]},"date_published":"2018-02-05T00:00:00Z","date_created":"2018-12-11T11:46:32Z","scopus_import":"1","publisher":"Springer Nature","intvolume":"         2","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2018","publication":"Nature Ecology and Evolution","date_updated":"2023-09-11T14:10:57Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9841"}]},"page":"557-566","pubrep_id":"969","citation":{"ieee":"M. Harrison <i>et al.</i>, “Hemimetabolous genomes reveal molecular basis of termite eusociality,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. 2018;2(3):557-566. doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>.","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>."},"day":"05","month":"02","file_date_updated":"2020-07-14T12:46:30Z","ddc":["576"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:46:30Z","access_level":"open_access","content_type":"application/pdf","checksum":"874953136ac125e65f37971d3cabc5b7","file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","relation":"main_file","creator":"system","file_size":3730583,"file_id":"4731","date_created":"2018-12-12T10:09:08Z"}],"has_accepted_license":"1","volume":2,"article_processing_charge":"No","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","author":[{"first_name":"Mark","last_name":"Harrison","full_name":"Harrison, Mark"},{"last_name":"Jongepier","full_name":"Jongepier, Evelien","first_name":"Evelien"},{"last_name":"Robertson","full_name":"Robertson, Hugh","first_name":"Hugh"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan"},{"last_name":"Chao","full_name":"Chao, Hsu","first_name":"Hsu"},{"full_name":"Childers, Christopher","last_name":"Childers","first_name":"Christopher"},{"first_name":"Huyen","last_name":"Dinh","full_name":"Dinh, Huyen"},{"full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni","first_name":"Harshavardhan"},{"last_name":"Dugan","full_name":"Dugan, Shannon","first_name":"Shannon"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"first_name":"Carolin","full_name":"Greiner, Carolin","last_name":"Greiner"},{"first_name":"Yi","full_name":"Han, Yi","last_name":"Han"},{"last_name":"Hu","full_name":"Hu, Haofu","first_name":"Haofu"},{"last_name":"Hughes","full_name":"Hughes, Daniel","first_name":"Daniel"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961"},{"first_name":"Karsten","last_name":"Kemena","full_name":"Kemena, Karsten"},{"first_name":"Lukas","last_name":"Kremer","full_name":"Kremer, Lukas"},{"full_name":"Lee, Sandra","last_name":"Lee","first_name":"Sandra"},{"last_name":"López Ezquerra","full_name":"López Ezquerra, Alberto","first_name":"Alberto"},{"last_name":"Mallet","full_name":"Mallet, Ludovic","first_name":"Ludovic"},{"full_name":"Monroy Kuhn, Jose","last_name":"Monroy Kuhn","first_name":"Jose"},{"last_name":"Moser","full_name":"Moser, Annabell","first_name":"Annabell"},{"first_name":"Shwetha","last_name":"Murali","full_name":"Murali, Shwetha"},{"full_name":"Muzny, Donna","last_name":"Muzny","first_name":"Donna"},{"first_name":"Saria","full_name":"Otani, Saria","last_name":"Otani"},{"last_name":"Piulachs","full_name":"Piulachs, Maria","first_name":"Maria"},{"first_name":"Monica","full_name":"Poelchau, Monica","last_name":"Poelchau"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"last_name":"Schaub","full_name":"Schaub, Florentine","first_name":"Florentine"},{"first_name":"Ayako","full_name":"Wada Katsumata, Ayako","last_name":"Wada Katsumata"},{"full_name":"Worley, Kim","last_name":"Worley","first_name":"Kim"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"full_name":"Poulsen, Michael","last_name":"Poulsen","first_name":"Michael"},{"first_name":"Richard","full_name":"Gibbs, Richard","last_name":"Gibbs"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"}],"_id":"448","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"issue":"3","doi":"10.1038/s41559-017-0459-1","publication_status":"published","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","status":"public"},{"date_created":"2018-12-11T11:46:32Z","scopus_import":"1","date_published":"2018-01-29T00:00:00Z","external_id":{"isi":["000423718600034"]},"publist_id":"7373","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"Public Library of Science","intvolume":"        14","year":"2018","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1127"},{"id":"7172","status":"public","relation":"dissertation_contains"},{"id":"8822","relation":"dissertation_contains","status":"public"}]},"date_updated":"2025-05-07T11:12:28Z","publication":"PLoS Genetics","oa_version":"Published Version","month":"01","file_date_updated":"2020-07-14T12:46:30Z","ddc":["581"],"citation":{"mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>, vol. 14, no. 1, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>.","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>.","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>","ieee":"T. Prat <i>et al.</i>, “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” <i>PLoS Genetics</i>, vol. 14, no. 1. Public Library of Science, 2018.","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. 2018;14(1). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1)."},"pubrep_id":"967","day":"29","article_processing_charge":"Yes","volume":14,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"4843","date_created":"2018-12-12T10:10:52Z","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","file_size":24709062,"relation":"main_file","creator":"system","date_updated":"2020-07-14T12:46:30Z","access_level":"open_access","content_type":"application/pdf","checksum":"0276d66788ec076f4924164a39e6a712"}],"doi":"10.1371/journal.pgen.1007177","abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"issue":"1","_id":"449","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","author":[{"first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","full_name":"Prat, Tomas"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"full_name":"Vasileva, Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","full_name":"Molnar, Gergely"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"last_name":"Schmid","full_name":"Schmid, Markus","first_name":"Markus"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"status":"public","publication_status":"published","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}]}]