[{"volume":90,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","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)"},"file":[{"date_updated":"2020-07-14T12:47:54Z","content_type":"application/pdf","checksum":"ab8130c6e68101f5a091d05324c36f08","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":537941,"file_name":"2020_EcologMono_Baskett.pdf","date_created":"2020-02-10T08:18:14Z","file_id":"7469"}],"oa_version":"Published Version","ddc":["570"],"month":"02","file_date_updated":"2020-07-14T12:47:54Z","day":"01","citation":{"apa":"Baskett, C., Schroeder, L., Weber, M. G., &#38; Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. <i>Ecological Monographs</i>. Wiley. <a href=\"https://doi.org/10.1002/ecm.1397\">https://doi.org/10.1002/ecm.1397</a>","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” <i>Ecological Monographs</i>, vol. 90, no. 1. Wiley, 2020.","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. <i>Ecological Monographs</i>. 2020;90(1). doi:<a href=\"https://doi.org/10.1002/ecm.1397\">10.1002/ecm.1397</a>","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397.","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” <i>Ecological Monographs</i>, vol. 90, no. 1, e01397, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/ecm.1397\">10.1002/ecm.1397</a>.","chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” <i>Ecological Monographs</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/ecm.1397\">https://doi.org/10.1002/ecm.1397</a>."},"ec_funded":1,"status":"public","publication_status":"published","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1557-7015"],"issn":["0012-9615"]},"doi":"10.1002/ecm.1397","issue":"1","abstract":[{"text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.","lang":"eng"}],"_id":"7236","author":[{"orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina"},{"first_name":"Lucy","full_name":"Schroeder, Lucy","last_name":"Schroeder"},{"first_name":"Marjorie G.","full_name":"Weber, Marjorie G.","last_name":"Weber"},{"full_name":"Schemske, Douglas W.","last_name":"Schemske","first_name":"Douglas W."}],"title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"        90","publisher":"Wiley","scopus_import":"1","date_created":"2020-01-07T12:47:07Z","external_id":{"isi":["000508511600001"]},"date_published":"2020-02-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"article_type":"original","article_number":"e01397","date_updated":"2023-09-05T15:43:19Z","publication":"Ecological Monographs","year":"2020","oa":1},{"intvolume":"        11","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SiHi"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"PreCl"}],"date_created":"2020-01-11T10:42:48Z","external_id":{"isi":["000551459000005"]},"date_published":"2020-01-10T00:00:00Z","date_updated":"2023-08-17T14:23:41Z","publication":"Nature Communications","article_type":"original","article_number":"195","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-function-for-potential-tumour-suppressor-in-brain-development/","description":"News on IST Homepage","relation":"press_release"}]},"oa":1,"year":"2020","file":[{"file_size":8063333,"relation":"main_file","creator":"dernst","file_name":"2020_NatureComm_Laukoter.pdf","content_type":"application/pdf","checksum":"ebf1ed522f4e0be8d94c939c1806a709","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-13T07:42:31Z","file_id":"7261"}],"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":11,"article_processing_charge":"No","has_accepted_license":"1","month":"01","file_date_updated":"2020-07-14T12:47:54Z","ddc":["570"],"day":"10","citation":{"chicago":"Laukoter, Susanne, Robert J Beattie, Florian Pauler, Nicole Amberg, Keiichi I. Nakayama, and Simon Hippenmeyer. “Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-019-14077-2\">https://doi.org/10.1038/s41467-019-14077-2</a>.","mla":"Laukoter, Susanne, et al. “Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development.” <i>Nature Communications</i>, vol. 11, 195, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-019-14077-2\">10.1038/s41467-019-14077-2</a>.","apa":"Laukoter, S., Beattie, R. J., Pauler, F., Amberg, N., Nakayama, K. I., &#38; Hippenmeyer, S. (2020). Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-14077-2\">https://doi.org/10.1038/s41467-019-14077-2</a>","ieee":"S. Laukoter, R. J. Beattie, F. Pauler, N. Amberg, K. I. Nakayama, and S. Hippenmeyer, “Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Laukoter S, Beattie RJ, Pauler F, Amberg N, Nakayama KI, Hippenmeyer S. 2020. Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. Nature Communications. 11, 195.","ama":"Laukoter S, Beattie RJ, Pauler F, Amberg N, Nakayama KI, Hippenmeyer S. Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-019-14077-2\">10.1038/s41467-019-14077-2</a>","short":"S. Laukoter, R.J. Beattie, F. Pauler, N. Amberg, K.I. Nakayama, S. Hippenmeyer, Nature Communications 11 (2020)."},"oa_version":"Published Version","project":[{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"},{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"7253","author":[{"orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keiichi I.","full_name":"Nakayama, Keiichi I.","last_name":"Nakayama"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development","doi":"10.1038/s41467-019-14077-2","abstract":[{"lang":"eng","text":"The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype."}]},{"alternative_title":["ISTA Thesis"],"year":"2020","oa":1,"related_material":{"record":[{"id":"6228","status":"public","relation":"part_of_dissertation"},{"id":"6486","relation":"part_of_dissertation","status":"public"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"id":"422","relation":"part_of_dissertation","status":"public"}]},"page":"174","date_updated":"2023-09-15T12:20:08Z","date_published":"2020-01-13T00:00:00Z","date_created":"2020-01-12T16:07:26Z","department":[{"_id":"BjHo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.","lang":"eng"}],"doi":"10.15479/AT:ISTA:7258","supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"title":"New approaches to reduce friction in turbulent pipe flow","author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","first_name":"Davide","full_name":"Scarselli, Davide","last_name":"Scarselli","orcid":"0000-0001-5227-4271"}],"_id":"7258","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines","grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425"},{"_id":"25136C54-B435-11E9-9278-68D0E5697425","grant_number":"HO 4393/1-2","name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents"}],"oa_version":"None","citation":{"ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","apa":"Scarselli, D. (2020). <i>New approaches to reduce friction in turbulent pipe flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7258\">https://doi.org/10.15479/AT:ISTA:7258</a>","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7258\">10.15479/AT:ISTA:7258</a>","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","mla":"Scarselli, Davide. <i>New Approaches to Reduce Friction in Turbulent Pipe Flow</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7258\">10.15479/AT:ISTA:7258</a>.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7258\">https://doi.org/10.15479/AT:ISTA:7258</a>."},"day":"13","ddc":["532"],"month":"01","file_date_updated":"2021-01-13T23:30:05Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"embargo_to":"open_access","file_id":"7259","date_created":"2020-01-12T15:57:14Z","file_name":"2020_Scarselli_Thesis.zip","creator":"dscarsel","relation":"source_file","file_size":26640830,"access_level":"closed","content_type":"application/zip","checksum":"4df1ab24e9896635106adde5a54615bf","date_updated":"2021-01-13T23:30:05Z"},{"date_created":"2020-01-12T15:56:14Z","file_id":"7260","checksum":"48659ab98e3414293c7a721385c2fd1c","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-01-13T23:30:05Z","relation":"main_file","file_size":8515844,"creator":"dscarsel","file_name":"2020_Scarselli_Thesis.pdf","embargo":"2021-01-12"}]},{"file":[{"creator":"rguseino","relation":"main_file","file_size":1315270,"file_name":"2020_NatureComm_Guseinov.pdf","date_updated":"2020-07-14T12:47:55Z","checksum":"7db23fef2f4cda712f17f1004116ddff","content_type":"application/pdf","access_level":"open_access","date_created":"2020-01-15T14:35:34Z","file_id":"7336"}],"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"},"article_processing_charge":"No","volume":11,"has_accepted_license":"1","ddc":["000"],"month":"01","file_date_updated":"2020-07-14T12:47:55Z","day":"13","citation":{"mla":"Guseinov, Ruslan, et al. “Programming Temporal Morphing of Self-Actuated Shells.” <i>Nature Communications</i>, vol. 11, 237, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-019-14015-2\">10.1038/s41467-019-14015-2</a>.","chicago":"Guseinov, Ruslan, Connor McMahan, Jesus Perez Rodriguez, Chiara Daraio, and Bernd Bickel. “Programming Temporal Morphing of Self-Actuated Shells.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-019-14015-2\">https://doi.org/10.1038/s41467-019-14015-2</a>.","short":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, B. Bickel, Nature Communications 11 (2020).","ama":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. Programming temporal morphing of self-actuated shells. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-019-14015-2\">10.1038/s41467-019-14015-2</a>","ista":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. 2020. Programming temporal morphing of self-actuated shells. Nature Communications. 11, 237.","apa":"Guseinov, R., McMahan, C., Perez Rodriguez, J., Daraio, C., &#38; Bickel, B. (2020). Programming temporal morphing of self-actuated shells. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-14015-2\">https://doi.org/10.1038/s41467-019-14015-2</a>","ieee":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, and B. Bickel, “Programming temporal morphing of self-actuated shells,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"7262","author":[{"last_name":"Guseinov","full_name":"Guseinov, Ruslan","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077"},{"full_name":"McMahan, Connor","last_name":"McMahan","first_name":"Connor"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","full_name":"Perez Rodriguez, Jesus","last_name":"Perez Rodriguez"},{"full_name":"Daraio, Chiara","last_name":"Daraio","first_name":"Chiara"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel"}],"title":"Programming temporal morphing of self-actuated shells","doi":"10.1038/s41467-019-14015-2","abstract":[{"lang":"eng","text":"Advances in shape-morphing materials, such as hydrogels, shape-memory polymers and light-responsive polymers have enabled prescribing self-directed deformations of initially flat geometries. However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses."}],"intvolume":"        11","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeBi"}],"scopus_import":"1","date_created":"2020-01-13T16:54:26Z","date_published":"2020-01-13T00:00:00Z","external_id":{"isi":["000511916800015"]},"date_updated":"2024-02-21T12:45:02Z","publication":"Nature Communications","article_type":"original","article_number":"237","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8366"},{"id":"7154","relation":"research_data","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/geometry-meets-time/","description":"News on IST Homepage"}]},"oa":1,"keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"year":"2020"},{"date_updated":"2021-01-11T15:25:48Z","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"publication":"Proceedings of the 2018 USENIX Annual Technical Conference","publication_identifier":{"isbn":["9781939133021"]},"page":"295-306","status":"public","publication_status":"published","_id":"7272","author":[{"first_name":"Maya","last_name":"Arbel-Raviv","full_name":"Arbel-Raviv, Maya"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Adam","last_name":"Morrison","full_name":"Morrison, Adam"}],"oa":1,"title":"Getting to the root of concurrent binary search tree performance","year":"2020","abstract":[{"lang":"eng","text":"Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple.\r\n\r\nWe focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap."}],"main_file_link":[{"url":"https://www.usenix.org/system/files/conference/atc18/atc18-arbel-raviv.pdf","open_access":"1"}],"publisher":"USENIX Association","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","article_processing_charge":"No","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","department":[{"_id":"DaAl"}],"day":"01","citation":{"chicago":"Arbel-Raviv, Maya, Trevor A Brown, and Adam Morrison. “Getting to the Root of Concurrent Binary Search Tree Performance.” In <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, 295–306. USENIX Association, 2020.","mla":"Arbel-Raviv, Maya, et al. “Getting to the Root of Concurrent Binary Search Tree Performance.” <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, USENIX Association, 2020, pp. 295–306.","apa":"Arbel-Raviv, M., Brown, T. A., &#38; Morrison, A. (2020). Getting to the root of concurrent binary search tree performance. In <i>Proceedings of the 2018 USENIX Annual Technical Conference</i> (pp. 295–306). Boston, MA, United States: USENIX Association.","ieee":"M. Arbel-Raviv, T. A. Brown, and A. Morrison, “Getting to the root of concurrent binary search tree performance,” in <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, Boston, MA, United States, 2020, pp. 295–306.","ama":"Arbel-Raviv M, Brown TA, Morrison A. Getting to the root of concurrent binary search tree performance. In: <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>. USENIX Association; 2020:295-306.","short":"M. Arbel-Raviv, T.A. Brown, A. Morrison, in:, Proceedings of the 2018 USENIX Annual Technical Conference, USENIX Association, 2020, pp. 295–306.","ista":"Arbel-Raviv M, Brown TA, Morrison A. 2020. Getting to the root of concurrent binary search tree performance. Proceedings of the 2018 USENIX Annual Technical Conference. USENIX: Annual Technical Conference, 295–306."},"conference":{"location":"Boston, MA, United States","start_date":"2018-07-11","end_date":"2018-07-13","name":"USENIX: Annual Technical Conference"},"scopus_import":"1","oa_version":"Published Version","date_created":"2020-01-14T07:27:08Z","date_published":"2020-01-01T00:00:00Z"},{"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Society for Neuroscience","intvolume":"        40","date_published":"2020-01-02T00:00:00Z","external_id":{"isi":["000505167600013"],"pmid":["31767677"]},"date_created":"2020-01-19T23:00:38Z","scopus_import":"1","department":[{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"131-142","article_type":"original","publication":"Journal of neuroscience","date_updated":"2023-08-17T14:25:23Z","year":"2020","oa":1,"has_accepted_license":"1","article_processing_charge":"No","volume":40,"file":[{"date_created":"2020-01-20T14:44:10Z","file_id":"7345","relation":"main_file","creator":"dernst","file_size":4460781,"file_name":"2020_JourNeuroscience_Piriya.pdf","content_type":"application/pdf","checksum":"92f5e8a47f454fc131fb94cd7f106e60","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z"}],"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"},"oa_version":"Published Version","citation":{"short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 131–142.","ista":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. 2020. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 40(1), 131–142.","ama":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of neuroscience</i>. 2020;40(1):131-142. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>","apa":"Piriya Ananda Babu, L., Wang, H. Y., Eguchi, K., Guillaud, L., &#38; Takahashi, T. (2020). Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>","ieee":"L. Piriya Ananda Babu, H. Y. Wang, K. Eguchi, L. Guillaud, and T. Takahashi, “Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission,” <i>Journal of neuroscience</i>, vol. 40, no. 1. Society for Neuroscience, pp. 131–142, 2020.","chicago":"Piriya Ananda Babu, Lashmi, Han Ying Wang, Kohgaku Eguchi, Laurent Guillaud, and Tomoyuki Takahashi. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>.","mla":"Piriya Ananda Babu, Lashmi, et al. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 131–42, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>."},"day":"02","file_date_updated":"2020-07-14T12:47:56Z","ddc":["570"],"pmid":1,"month":"01","publication_status":"published","status":"public","publication_identifier":{"eissn":["15292401"]},"abstract":[{"lang":"eng","text":"Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission."}],"issue":"1","doi":"10.1523/JNEUROSCI.1571-19.2019","title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","author":[{"last_name":"Piriya Ananda Babu","full_name":"Piriya Ananda Babu, Lashmi","first_name":"Lashmi"},{"first_name":"Han Ying","full_name":"Wang, Han Ying","last_name":"Wang"},{"orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"_id":"7339"},{"file":[{"date_created":"2020-11-19T11:27:10Z","file_id":"8776","content_type":"application/pdf","checksum":"0cd8be386fa219db02845b7c3991ce04","access_level":"open_access","date_updated":"2020-11-19T11:27:10Z","success":1,"file_size":561749,"relation":"main_file","creator":"dernst","file_name":"2020_EcologyLetters_Milutinovic.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)"},"has_accepted_license":"1","volume":23,"article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., &#38; Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13458\">https://doi.org/10.1111/ele.13458</a>","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” <i>Ecology Letters</i>, vol. 23, no. 3. Wiley, pp. 565–574, 2020.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. <i>Ecology Letters</i>. 2020;23(3):565-574. doi:<a href=\"https://doi.org/10.1111/ele.13458\">10.1111/ele.13458</a>","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” <i>Ecology Letters</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/ele.13458\">https://doi.org/10.1111/ele.13458</a>.","mla":"Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” <i>Ecology Letters</i>, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:<a href=\"https://doi.org/10.1111/ele.13458\">10.1111/ele.13458</a>."},"day":"01","file_date_updated":"2020-11-19T11:27:10Z","ddc":["570"],"month":"03","oa_version":"Published Version","publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"status":"public","publication_status":"published","acknowledgement":"We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). ","ec_funded":1,"title":"Social immunity modulates competition between coinfecting pathogens","author":[{"first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758"},{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","last_name":"Stock","full_name":"Stock, Miriam"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"_id":"7343","abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level."}],"issue":"3","doi":"10.1111/ele.13458","publisher":"Wiley","intvolume":"        23","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"},{"_id":"KrCh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2020-03-01T00:00:00Z","external_id":{"isi":["000507515900001"]},"date_created":"2020-01-20T13:32:12Z","acknowledged_ssus":[{"_id":"LifeSc"}],"scopus_import":"1","publication":"Ecology Letters","date_updated":"2023-09-05T16:04:49Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/","relation":"press_release"}],"record":[{"relation":"research_data","status":"public","id":"13060"}]},"page":"565-574","article_type":"letter_note","oa":1,"year":"2020"},{"article_number":"21","publication":"Proceedings of the 23rd International Conference on Principles of Distributed Systems","date_updated":"2023-02-23T13:05:49Z","year":"2020","alternative_title":["LIPIcs"],"oa":1,"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       153","date_published":"2020-02-10T00:00:00Z","external_id":{"arxiv":["1906.00110"]},"date_created":"2020-01-21T16:00:26Z","scopus_import":"1","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to \"one-shot games\"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. "}],"doi":"10.4230/LIPIcs.OPODIS.2019.21","title":"The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game","author":[{"full_name":"Schmid, Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","orcid":"0000-0002-6978-7329"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"_id":"7346","has_accepted_license":"1","volume":153,"article_processing_charge":"No","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_created":"2020-03-23T09:14:06Z","file_id":"7608","relation":"main_file","creator":"dernst","file_size":630752,"file_name":"2019_LIPIcS_Schmid.pdf","content_type":"application/pdf","checksum":"9a91916ac2c21ab42458fcda39ef0b8d","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z"}],"arxiv":1,"oa_version":"Preprint","conference":{"end_date":"2019-12-19","location":"Neuchâtel, Switzerland","start_date":"2019-12-17","name":"OPODIS: International Conference on Principles of Distributed Systems"},"citation":{"ama":"Schmid L, Chatterjee K, Schmid S. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In: <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>","ista":"Schmid L, Chatterjee K, Schmid S. 2020. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. Proceedings of the 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 21.","short":"L. Schmid, K. Chatterjee, S. Schmid, in:, Proceedings of the 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"L. Schmid, K. Chatterjee, and S. Schmid, “The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game,” in <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Neuchâtel, Switzerland, 2020, vol. 153.","apa":"Schmid, L., Chatterjee, K., &#38; Schmid, S. (2020). The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i> (Vol. 153). Neuchâtel, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>","mla":"Schmid, Laura, et al. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, vol. 153, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>.","chicago":"Schmid, Laura, Krishnendu Chatterjee, and Stefan Schmid. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Vol. 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>."},"day":"10","ddc":["000"],"month":"02","file_date_updated":"2020-07-14T12:47:56Z"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       152","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-15T00:00:00Z","external_id":{"arxiv":["1910.06097"]},"date_created":"2020-01-21T11:22:21Z","scopus_import":1,"publication":"28th EACSL Annual Conference on Computer Science Logic","date_updated":"2021-01-12T08:13:12Z","article_number":"20","oa":1,"alternative_title":["LIPIcs"],"year":"2020","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":"7349","date_created":"2020-01-21T11:21:04Z","file_name":"main.pdf","creator":"bkragl","file_size":617206,"relation":"main_file","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","checksum":"b9a691d658d075c6369d3304d17fb818","content_type":"application/pdf"}],"arxiv":1,"has_accepted_license":"1","volume":152,"article_processing_charge":"No","citation":{"ista":"Ferrere T, Henzinger TA, Kragl B. 2020. Monitoring event frequencies. 28th EACSL Annual Conference on Computer Science Logic. CSL: Computer Science Logic, LIPIcs, vol. 152, 20.","short":"T. Ferrere, T.A. Henzinger, B. Kragl, in:, 28th EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ama":"Ferrere T, Henzinger TA, Kragl B. Monitoring event frequencies. In: <i>28th EACSL Annual Conference on Computer Science Logic</i>. Vol 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>","ieee":"T. Ferrere, T. A. Henzinger, and B. Kragl, “Monitoring event frequencies,” in <i>28th EACSL Annual Conference on Computer Science Logic</i>, Barcelona, Spain, 2020, vol. 152.","apa":"Ferrere, T., Henzinger, T. A., &#38; Kragl, B. (2020). Monitoring event frequencies. In <i>28th EACSL Annual Conference on Computer Science Logic</i> (Vol. 152). Barcelona, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>","mla":"Ferrere, Thomas, et al. “Monitoring Event Frequencies.” <i>28th EACSL Annual Conference on Computer Science Logic</i>, vol. 152, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Bernhard Kragl. “Monitoring Event Frequencies.” In <i>28th EACSL Annual Conference on Computer Science Logic</i>, Vol. 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>."},"day":"15","month":"01","ddc":["000"],"file_date_updated":"2020-07-14T12:47:56Z","oa_version":"Published Version","conference":{"end_date":"2020-01-16","location":"Barcelona, Spain","start_date":"2020-01-13","name":"CSL: Computer Science Logic"},"publication_identifier":{"isbn":["9783959771320"],"issn":["1868-8969"]},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_status":"published","status":"public","title":"Monitoring event frequencies","author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"}],"_id":"7348","abstract":[{"text":"The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. ","lang":"eng"}],"doi":"10.4230/LIPIcs.CSL.2020.20"},{"oa":1,"year":"2020","date_updated":"2023-08-17T14:21:45Z","publication":"Frontiers in Plant Science","article_number":"1680","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EvBe"}],"date_created":"2020-01-22T15:23:57Z","scopus_import":"1","external_id":{"isi":["000511376000001"]},"date_published":"2020-01-22T00:00:00Z","publisher":"Frontiers Media","intvolume":"        10","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"7350","title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","author":[{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"orcid":"0000-0003-4675-6893","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"full_name":"Doonan, John H.","last_name":"Doonan","first_name":"John H."},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","full_name":"Cavallari, Nicola","last_name":"Cavallari"}],"doi":"10.3389/fpls.2019.01680","abstract":[{"lang":"eng","text":"The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition."}],"publication_identifier":{"issn":["1664-462X"]},"status":"public","publication_status":"published","ddc":["580"],"file_date_updated":"2020-07-14T12:47:56Z","month":"01","citation":{"ama":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. 2020;10. doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>","ista":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. 2020. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. 10, 1680.","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020).","apa":"Nibau, C., Gallemi, M., Dadarou, D., Doonan, J. H., &#38; Cavallari, N. (2020). Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>","ieee":"C. Nibau, M. Gallemi, D. Dadarou, J. H. Doonan, and N. Cavallari, “Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2,” <i>Frontiers in Plant Science</i>, vol. 10. Frontiers Media, 2020.","mla":"Nibau, Candida, et al. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>, vol. 10, 1680, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>.","chicago":"Nibau, Candida, Marçal Gallemi, Despoina Dadarou, John H. Doonan, and Nicola Cavallari. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>."},"day":"22","oa_version":"Published Version","file":[{"file_name":"2020_FrontiersPlantScience_Nibau.pdf","creator":"dernst","relation":"main_file","file_size":1951438,"date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","content_type":"application/pdf","checksum":"d1f92e60a713fbd15097ce895e5c7ccb","file_id":"7366","date_created":"2020-01-27T09:07:02Z"}],"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"},"article_processing_charge":"No","volume":10,"has_accepted_license":"1"},{"department":[{"_id":"BjHo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000552271200011"],"arxiv":["1908.00587"]},"date_published":"2020-01-17T00:00:00Z","scopus_import":"1","date_created":"2020-01-26T23:00:35Z","intvolume":"        11","publisher":"Elsevier","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2020","publication":"SoftwareX","date_updated":"2023-08-17T14:29:59Z","article_type":"original","article_number":"100395","day":"17","citation":{"ieee":"J. M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, and M. Avila, “nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow,” <i>SoftwareX</i>, vol. 11. Elsevier, 2020.","apa":"Lopez Alonso, J. M., Feldmann, D., Rampp, M., Vela-Martín, A., Shi, L., &#38; Avila, M. (2020). nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>","ista":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. 2020. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 11, 100395.","ama":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. 2020;11. doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>","short":"J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020).","mla":"Lopez Alonso, Jose M., et al. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>, vol. 11, 100395, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>.","chicago":"Lopez Alonso, Jose M, Daniel Feldmann, Markus Rampp, Alberto Vela-Martín, Liang Shi, and Marc Avila. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>."},"ddc":["000"],"month":"01","file_date_updated":"2020-07-14T12:47:56Z","oa_version":"Published Version","file":[{"creator":"dernst","relation":"main_file","file_size":679707,"file_name":"2020_SoftwareX_Lopez.pdf","content_type":"application/pdf","checksum":"2af1a1a3cc33557b345145276f221668","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-01-27T07:32:46Z","file_id":"7365"}],"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"},"arxiv":1,"has_accepted_license":"1","article_processing_charge":"No","volume":11,"author":[{"orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Feldmann","full_name":"Feldmann, Daniel"},{"last_name":"Rampp","full_name":"Rampp, Markus","first_name":"Markus"},{"last_name":"Vela-Martín","full_name":"Vela-Martín, Alberto","first_name":"Alberto"},{"full_name":"Shi, Liang","last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","_id":"7364","abstract":[{"lang":"eng","text":"We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided."}],"doi":"10.1016/j.softx.2019.100395","publication_identifier":{"eissn":["23527110"]},"status":"public","publication_status":"published"},{"date_updated":"2023-08-17T14:35:22Z","publication":"Journal of Computational Neuroscience","page":"85-102","article_type":"original","oa":1,"keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"year":"2020","publisher":"Springer Nature","intvolume":"        48","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SaSi"}],"date_created":"2020-01-28T10:34:00Z","scopus_import":"1","date_published":"2020-02-01T00:00:00Z","external_id":{"isi":["000515321800006"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"eissn":["1573-6873"],"issn":["0929-5313"]},"ec_funded":1,"acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","status":"public","publication_status":"published","_id":"7369","title":"Multiscale relevance and informative encoding in neuronal spike trains","author":[{"last_name":"Cubero","full_name":"Cubero, Ryan J","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867"},{"first_name":"Matteo","full_name":"Marsili, Matteo","last_name":"Marsili"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"}],"doi":"10.1007/s10827-020-00740-x","abstract":[{"lang":"eng","text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate."}],"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":"10827_2020_740_MOESM1_ESM.pdf","creator":"rcubero","relation":"supplementary_material","file_size":1941355,"access_level":"open_access","checksum":"036e9451d6cd0c190ad25791bf82393b","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z","file_id":"7380","date_created":"2020-01-28T09:31:09Z"},{"file_id":"7381","date_created":"2020-01-28T09:31:09Z","access_level":"open_access","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","relation":"main_file","creator":"rcubero","file_size":3257880}],"volume":48,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","ddc":["004","519","570"],"month":"02","file_date_updated":"2020-07-14T12:47:56Z","citation":{"chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>.","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer Nature, 2020, pp. 85–102, doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>.","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>, vol. 48. Springer Nature, pp. 85–102, 2020.","apa":"Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102. doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>"},"day":"01","oa_version":"Published Version"},{"doi":"10.15479/AT:ISTA:7383","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"year":"2020","_id":"7383","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","oa":1,"author":[{"full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560"}],"related_material":{"record":[{"id":"7652","relation":"used_in_publication","status":"public"}]},"status":"public","date_updated":"2024-02-21T12:42:31Z","date_created":"2020-01-28T10:41:49Z","oa_version":"Published Version","date_published":"2020-01-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","file_date_updated":"2020-07-14T12:47:57Z","citation":{"ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>","short":"R. Grah, (2020).","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>.","mla":"Grah, Rok. <i>Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>."},"day":"28","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","type":"research_data","contributor":[{"contributor_type":"project_leader","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2020-01-28T10:39:40Z","file_id":"7384","date_updated":"2020-07-14T12:47:57Z","checksum":"9d292cf5207b3829225f44c044cdb3fd","content_type":"application/zip","access_level":"open_access","file_size":73363365,"relation":"main_file","creator":"rgrah","file_name":"Scripts.zip"},{"file_name":"READ_ME_MAIN.txt","relation":"main_file","creator":"rgrah","file_size":962,"access_level":"open_access","checksum":"4076ceab32ef588cc233802bab24c1ab","content_type":"text/plain","date_updated":"2020-07-14T12:47:57Z","file_id":"7385","date_created":"2020-01-28T10:39:30Z"}]},{"publisher":"Springer Nature","intvolume":"         5","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaLo"}],"date_created":"2020-01-28T16:14:41Z","scopus_import":"1","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"date_published":"2020-01-20T00:00:00Z","date_updated":"2023-10-06T12:22:38Z","publication":"Nature Microbiology","page":"407-417","article_type":"letter_note","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14280"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","description":"News on IST Homepage"}]},"oa":1,"year":"2020","article_processing_charge":"No","volume":5,"pmid":1,"month":"01","citation":{"chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>","ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417."},"day":"20","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2058-5276"]},"ec_funded":1,"publication_status":"published","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","status":"public","_id":"7387","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","author":[{"last_name":"Baranova","full_name":"Baranova, Natalia S.","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124"},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp"},{"last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M."},{"first_name":"Carlos","last_name":"Alfonso","full_name":"Alfonso, Carlos"},{"last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Germán","full_name":"Rivas, Germán","last_name":"Rivas"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1038/s41564-019-0657-5","abstract":[{"text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.","lang":"eng"}]},{"publication_identifier":{"issn":["0294-1449"]},"status":"public","publication_status":"published","title":"Nondivergence form quasilinear heat equations driven by space-time white noise","author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"_id":"7388","abstract":[{"lang":"eng","text":"We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants."}],"issue":"3","doi":"10.1016/j.anihpc.2020.01.003","arxiv":1,"volume":37,"article_processing_charge":"No","citation":{"mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>.","chicago":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>.","apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>, vol. 37, no. 3. Elsevier, pp. 663–682, 2020.","ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>. 2020;37(3):663-682. doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>","ista":"Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 37(3), 663–682.","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682."},"day":"01","month":"05","oa_version":"Preprint","publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","date_updated":"2023-08-17T14:35:46Z","page":"663-682","article_type":"original","oa":1,"year":"2020","publisher":"Elsevier","intvolume":"        37","main_file_link":[{"url":"https://arxiv.org/abs/1902.07635","open_access":"1"}],"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"JaMa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["1902.07635"],"isi":["000531049800007"]},"date_published":"2020-05-01T00:00:00Z","date_created":"2020-01-29T09:39:41Z","scopus_import":"1"},{"department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-08-01T00:00:00Z","external_id":{"arxiv":["2002.00859"],"isi":["000551418100018"]},"date_created":"2020-01-29T10:20:46Z","publisher":"American Mathematical Society","intvolume":"       373","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.00859"}],"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2020","keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"publication":"Transactions of the American Mathematical Society","date_updated":"2023-08-17T14:31:03Z","page":"5855-5883","article_type":"original","citation":{"short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883.","ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. 2020;373(8):5855-5883. doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020.","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2020. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>.","mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>."},"day":"01","month":"08","ddc":["515"],"oa_version":"Preprint","arxiv":1,"volume":373,"article_processing_charge":"No","title":"Isometric study of Wasserstein spaces - the real line","author":[{"first_name":"Gyorgy Pal","full_name":"Geher, Gyorgy Pal","last_name":"Geher"},{"first_name":"Tamas","full_name":"Titkos, Tamas","last_name":"Titkos"},{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511"}],"_id":"7389","abstract":[{"lang":"eng","text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R))."}],"issue":"8","doi":"10.1090/tran/8113","publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"project":[{"grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability"}],"status":"public","publication_status":"published","ec_funded":1},{"oa_version":"Preprint","month":"06","citation":{"mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. LNM. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>.","ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in <i>Geometric Aspects of Functional Analysis</i>, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","apa":"Akopyan, A., &#38; Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag &#38; E. Milman (Eds.), <i>Geometric Aspects of Functional Analysis</i> (Vol. 2256, pp. 1–27). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>","short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27.","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. <i>Geometric Aspects of Functional Analysis</i>. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27."},"day":"21","volume":2256,"article_processing_charge":"No","arxiv":1,"doi":"10.1007/978-3-030-36020-7_1","abstract":[{"text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean  space,  motivated  by  the  famous  theorem  of  Gromov  about  the  waist  of  radially symmetric Gaussian measures.  In particular, it turns our possible to extend Gromov’s original result  to  the  case  of  not  necessarily  radially  symmetric  Gaussian  measure.   We  also  provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe  use  a  simpler  form  of  Gromov’s  pancake  argument  to  produce  some  estimates  of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures.","lang":"eng"}],"editor":[{"first_name":"Bo'az","full_name":"Klartag, Bo'az","last_name":"Klartag"},{"first_name":"Emanuel","full_name":"Milman, Emanuel","last_name":"Milman"}],"_id":"74","title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"ec_funded":1,"status":"public","publication_status":"published","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["16179692"],"issn":["00758434"],"eisbn":["9783030360207"],"isbn":["9783030360191"]},"date_created":"2018-12-11T11:44:29Z","scopus_import":"1","external_id":{"isi":["000557689300003"],"arxiv":["1808.07350"]},"date_published":"2020-06-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"book_chapter","isi":1,"publisher":"Springer Nature","intvolume":"      2256","main_file_link":[{"url":"https://arxiv.org/abs/1808.07350","open_access":"1"}],"series_title":"LNM","year":"2020","oa":1,"page":"1-27","date_updated":"2023-08-17T13:48:31Z","publication":"Geometric Aspects of Functional Analysis"},{"status":"public","publication_status":"published","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"doi":"10.1016/bs.ctdb.2019.07.001","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"editor":[{"first_name":"Lilianna ","full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel"}],"_id":"7410","title":"Mechanisms of zebrafish epiboly: A current view","author":[{"first_name":"Ashley E.E.","full_name":"Bruce, Ashley E.E.","last_name":"Bruce"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","volume":136,"oa_version":"None","month":"01","citation":{"chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in <i>Gastrulation: From Embryonic Pattern to Form</i>, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","apa":"Bruce, A. E. E., &#38; Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), <i>Gastrulation: From Embryonic Pattern to Form</i> (Vol. 136, pp. 319–341). Elsevier. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. <i>Gastrulation: From Embryonic Pattern to Form</i>. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>"},"day":"01","page":"319-341","date_updated":"2024-02-22T13:23:09Z","publication":"Gastrulation: From Embryonic Pattern to Form","year":"2020","language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_chapter","isi":1,"publisher":"Elsevier","intvolume":"       136","series_title":"Current Topics in Developmental Biology","date_created":"2020-01-30T09:24:06Z","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","external_id":{"isi":["000611830600012"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}]},{"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Taylor & Francis","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"intvolume":"        15","date_created":"2020-01-30T10:12:04Z","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"article_number":"1687175","article_type":"original","date_updated":"2023-10-17T09:01:48Z","publication":"Plant Signaling & Behavior","year":"2020","oa":1,"volume":15,"article_processing_charge":"No","oa_version":"Submitted Version","pmid":1,"month":"01","citation":{"mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>","short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020."},"day":"01","status":"public","publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"doi":"10.1080/15592324.2019.1687175","abstract":[{"lang":"eng","text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements."}],"issue":"1","_id":"7416","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","author":[{"first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593"},{"first_name":"U.","last_name":"Krämer","full_name":"Krämer, U."}]},{"date_updated":"2023-09-06T15:23:04Z","publication":"Plant Signaling & Behavior","article_number":"e1687185","article_type":"original","oa":1,"year":"2020","publisher":"Informa UK Limited","intvolume":"        15","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"date_created":"2020-01-30T10:14:14Z","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"publication_identifier":{"issn":["1559-2324"]},"publication_status":"published","status":"public","_id":"7417","title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","author":[{"orcid":"0000-0002-4566-0593","last_name":"Sinclair","full_name":"Sinclair, Scott A","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gille","full_name":"Gille, S.","first_name":"S."},{"last_name":"Pauly","full_name":"Pauly, M.","first_name":"M."},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"doi":"10.1080/15592324.2019.1687185","abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"issue":"1","volume":15,"article_processing_charge":"No","month":"01","pmid":1,"citation":{"short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020.","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>."},"day":"01","oa_version":"Submitted Version"}]