[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor"}],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"oa":1,"type":"research_data","date_published":"2020-12-10T00:00:00Z","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"ddc":["570"],"date_updated":"2024-02-21T12:41:42Z","status":"public","department":[{"_id":"GaTk"}],"month":"12","day":"10","doi":"10.15479/AT:ISTA:8930","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-12-09T15:00:19Z","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","contributor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik"},{"first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"citation":{"ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","short":"B. Kavcic, (2020).","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>"},"year":"2020","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"file":[{"relation":"main_file","file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","file_name":"PLoSCompBiol2020_datarep.zip","success":1,"access_level":"open_access","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","content_type":"application/zip","creator":"bkavcic","file_id":"8932"}],"date_created":"2020-12-09T15:04:02Z","has_accepted_license":"1","_id":"8930"},{"day":"01","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"has_accepted_license":"1","issue":"9","publisher":"Elsevier","pmid":1,"external_id":{"pmid":["33264621"],"isi":["000595658100018"]},"date_published":"2020-12-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["580"],"status":"public","month":"12","isi":1,"article_type":"original","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","publication_identifier":{"eissn":["22111247"]},"doi":"10.1016/j.celrep.2020.108463","scopus_import":"1","file_date_updated":"2020-12-14T07:33:39Z","oa_version":"Published Version","article_processing_charge":"Yes","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","publication_status":"published","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"article_number":"108463","year":"2020","citation":{"ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. 2020;33(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>","ieee":"S. Tan <i>et al.</i>, “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” <i>Cell Reports</i>, vol. 33, no. 9. Elsevier, 2020.","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>, vol. 33, no. 9, 108463, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>.","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>"},"_id":"8943","date_created":"2020-12-13T23:01:21Z","file":[{"date_created":"2020-12-14T07:33:39Z","relation":"main_file","file_size":8056434,"date_updated":"2020-12-14T07:33:39Z","access_level":"open_access","success":1,"file_name":"2020_CellReports_Tan.pdf","checksum":"ed18cba0fb48ed2e789381a54cc21904","file_id":"8948","creator":"dernst","content_type":"application/pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"full_name":"Di Donato, Martin","last_name":"Di Donato","first_name":"Martin"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous"},{"last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"first_name":"Jie","last_name":"Liu","full_name":"Liu, Jie"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","relation":"press_release","description":"News on IST Homepage"}]},"oa":1,"volume":33,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"intvolume":"        33","publication":"Cell Reports","ec_funded":1,"date_updated":"2023-11-16T13:03:31Z","department":[{"_id":"JiFr"}]},{"department":[{"_id":"JoFi"}],"publication":"Physical Review B","date_updated":"2023-08-24T10:53:36Z","arxiv":1,"intvolume":"       102","oa":1,"volume":102,"author":[{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin"},{"last_name":"Kopčík","first_name":"M.","full_name":"Kopčík, M."},{"first_name":"P.","last_name":"Szabó","full_name":"Szabó, P."},{"full_name":"Samuely, T.","first_name":"T.","last_name":"Samuely"},{"last_name":"Kačmarčík","first_name":"J.","full_name":"Kačmarčík, J."},{"full_name":"Neilinger, P.","last_name":"Neilinger","first_name":"P."},{"full_name":"Grajcar, M.","last_name":"Grajcar","first_name":"M."},{"first_name":"P.","last_name":"Samuely","full_name":"Samuely, P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8944","date_created":"2020-12-13T23:01:21Z","year":"2020","article_number":"180508","citation":{"ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>"},"abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.","lang":"eng"}],"publication_status":"published","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","article_processing_charge":"No","oa_version":"Preprint","doi":"10.1103/PhysRevB.102.180508","main_file_link":[{"url":"https://arxiv.org/abs/2011.04329","open_access":"1"}],"scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","month":"11","isi":1,"status":"public","language":[{"iso":"eng"}],"date_published":"2020-11-01T00:00:00Z","external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]},"type":"journal_article","publisher":"American Physical Society","issue":"18","quality_controlled":"1","day":"01"},{"intvolume":"         9","department":[{"_id":"SiHi"}],"publication":"Cells","date_updated":"2023-08-24T10:57:48Z","ec_funded":1,"author":[{"last_name":"Zhang","first_name":"Xuying","full_name":"Zhang, Xuying"},{"last_name":"Mennicke","first_name":"Christine V.","full_name":"Mennicke, Christine V."},{"first_name":"Guanxi","last_name":"Xiao","full_name":"Xiao, Guanxi"},{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J"},{"first_name":"Mansoor","last_name":"Haider","full_name":"Haider, Mansoor"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Ghashghaei, H. Troy","first_name":"H. Troy","last_name":"Ghashghaei"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":9,"article_number":"2662","year":"2020","citation":{"apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>"},"abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"_id":"8949","date_created":"2020-12-14T08:04:03Z","file":[{"date_created":"2020-12-14T08:09:43Z","relation":"main_file","date_updated":"2020-12-14T08:09:43Z","file_size":3504525,"file_name":"2020_Cells_Zhang.pdf","access_level":"open_access","success":1,"checksum":"5095cbdc728c9a510c5761cf60a8861c","creator":"dernst","file_id":"8950","content_type":"application/pdf"}],"doi":"10.3390/cells9122662","article_type":"original","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","publication_identifier":{"issn":["2073-4409"]},"publication_status":"published","title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","file_date_updated":"2020-12-14T08:09:43Z","article_processing_charge":"No","oa_version":"Published Version","language":[{"iso":"eng"}],"ddc":["570"],"month":"12","isi":1,"status":"public","publisher":"MDPI","date_published":"2020-12-11T00:00:00Z","external_id":{"isi":["000601787300001"]},"type":"journal_article","issue":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","call_identifier":"FWF"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"}],"day":"11","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"year":"2020","citation":{"ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","short":"A.A. Nagy-Staron, (2020).","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>."},"_id":"8951","file":[{"content_type":"text/plain","file_id":"8952","creator":"bkavcic","checksum":"f57862aeee1690c7effd2b1117d40ed1","file_name":"readme.txt","access_level":"open_access","success":1,"file_size":523,"relation":"main_file","date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z"},{"file_name":"GRNs Research depository.gb","success":1,"access_level":"open_access","date_updated":"2020-12-20T22:01:44Z","date_created":"2020-12-20T22:01:44Z","file_size":379228,"relation":"main_file","creator":"bkavcic","file_id":"8954","content_type":"application/octet-stream","checksum":"f2c6d5232ec6d551b6993991e8689e9f"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","date_created":"2020-12-20T10:00:26Z","day":"21","doi":"10.15479/AT:ISTA:8951","file_date_updated":"2020-12-20T22:01:44Z","article_processing_charge":"No","oa_version":"Published Version","contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron","contributor_type":"project_member"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Tomasek","first_name":"Kathrin"},{"first_name":"Caroline","contributor_type":"project_member","last_name":"Caruso Carter"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Paixão","first_name":"Tiago"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","contributor_type":"project_manager","first_name":"Calin C"}],"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"ddc":["570"],"status":"public","date_updated":"2024-02-21T12:41:57Z","month":"12","department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Nagy-Staron","first_name":"Anna A","full_name":"Nagy-Staron, Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9283"}]},"oa":1,"date_published":"2020-12-21T00:00:00Z","type":"research_data"},{"citation":{"short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>.","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070."},"year":"2020","article_number":"558070","abstract":[{"lang":"eng","text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies."}],"date_created":"2020-12-20T23:01:18Z","file":[{"file_name":"2020_Frontiers_Rizzo.pdf","access_level":"open_access","success":1,"file_size":13380030,"date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-21T10:37:50Z","relation":"main_file","content_type":"application/pdf","file_id":"8961","creator":"dernst","checksum":"ef9515b28c5619b7126c0f347958bcb3"}],"_id":"8955","scopus_import":"1","doi":"10.3389/fphys.2020.558070","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","publication_identifier":{"eissn":["1664042X"]},"article_type":"original","publication_status":"published","title":"Network physiology of cortico–muscular interactions","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-12-21T10:37:50Z","intvolume":"        11","department":[{"_id":"GaTk"}],"date_updated":"2023-08-24T11:00:45Z","ec_funded":1,"publication":"Frontiers in Physiology","author":[{"full_name":"Rizzo, Rossella","last_name":"Rizzo","first_name":"Rossella"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"first_name":"Jilin W.J.L.","last_name":"Wang","full_name":"Wang, Jilin W.J.L."},{"first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch","last_name":"Ivanov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":11,"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"26","quality_controlled":"1","ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"month":"11","status":"public","pmid":1,"publisher":"Frontiers","type":"journal_article","external_id":{"pmid":["33324233"],"isi":["000596849400001"]},"date_published":"2020-11-26T00:00:00Z"},{"doi":"10.1016/j.devcel.2020.10.016","scopus_import":"1","article_type":"original","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8).","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","publication_status":"published","oa_version":"None","article_processing_charge":"No","year":"2020","citation":{"ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. 2020;55(6):695-706. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>","ieee":"B. G. Godard <i>et al.</i>, “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” <i>Developmental Cell</i>, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., &#38; Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>","chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>."},"abstract":[{"lang":"eng","text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation."}],"_id":"8957","date_created":"2020-12-20T23:01:19Z","author":[{"id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G","first_name":"Benoit G","last_name":"Godard"},{"first_name":"Rémi","last_name":"Dumollard","full_name":"Dumollard, Rémi"},{"full_name":"Munro, Edwin","first_name":"Edwin","last_name":"Munro"},{"full_name":"Chenevert, Janet","first_name":"Janet","last_name":"Chenevert"},{"full_name":"Hebras, Céline","first_name":"Céline","last_name":"Hebras"},{"first_name":"Alex","last_name":"Mcdougall","full_name":"Mcdougall, Alex"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/relaxing-cell-divisions/"}]},"volume":55,"intvolume":"        55","department":[{"_id":"CaHe"}],"publication":"Developmental Cell","date_updated":"2023-08-24T11:01:22Z","page":"695-706","day":"21","quality_controlled":"1","issue":"6","publisher":"Elsevier","pmid":1,"external_id":{"isi":["000600665700008"],"pmid":["33207225"]},"date_published":"2020-12-21T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"month":"12","isi":1,"status":"public"},{"ec_funded":1,"date_updated":"2024-08-07T07:16:53Z","department":[{"_id":"MiLe"}],"degree_awarded":"PhD","oa":1,"related_material":{"record":[{"id":"5886","relation":"part_of_dissertation","status":"public"},{"id":"1120","status":"public","relation":"part_of_dissertation"},{"id":"8587","status":"public","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Li","first_name":"Xiang","full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","success":1,"date_updated":"2020-12-22T10:55:56Z","date_created":"2020-12-22T10:55:56Z","file_size":3622305,"relation":"main_file","content_type":"application/pdf","file_id":"8967","creator":"xli","checksum":"3994c54a1241451d561db1d4f43bad30"},{"relation":"source_file","file_size":4018859,"date_created":"2020-12-22T10:56:03Z","date_updated":"2020-12-30T07:18:03Z","access_level":"closed","file_name":"THESIS_Xiang_Li.zip","checksum":"0954ecfc5554c05615c14de803341f00","creator":"xli","file_id":"8968","content_type":"application/x-zip-compressed"}],"date_created":"2020-12-21T09:44:30Z","_id":"8958","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"supervisor":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"}],"citation":{"mla":"Li, Xiang. <i>Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>.","apa":"Li, X. (2020). <i>Rotation of coupled cold molecules in the presence of a many-body environment</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>"},"year":"2020","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2020-12-30T07:18:03Z","publication_status":"published","title":"Rotation of coupled cold molecules in the presence of a many-body environment","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8958","status":"public","month":"12","alternative_title":["ISTA Thesis"],"ddc":["539"],"language":[{"iso":"eng"}],"type":"dissertation","date_published":"2020-12-21T00:00:00Z","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","project":[{"call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"day":"21","page":"125"},{"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12","publisher":"Springer Nature","type":"journal_article","external_id":{"isi":["000603078000003"]},"date_published":"2020-12-22T00:00:00Z","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"22","quality_controlled":"1","intvolume":"        11","date_updated":"2023-08-24T11:01:50Z","publication":"Nature Communications","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"volume":11,"oa":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"citation":{"ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>"},"year":"2020","article_number":"6437","file":[{"checksum":"55d43ea0061cc4027ba45e966e1db8cc","creator":"dernst","file_id":"8975","content_type":"application/pdf","date_created":"2020-12-28T08:16:10Z","relation":"main_file","date_updated":"2020-12-28T08:16:10Z","file_size":3958727,"success":1,"access_level":"open_access","file_name":"2020_NatureComm_Faessler.pdf"}],"date_created":"2020-12-23T08:25:45Z","_id":"8971","publication_identifier":{"issn":["2041-1723"]},"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","article_type":"original","scopus_import":"1","doi":"10.1038/s41467-020-20286-x","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-12-28T08:16:10Z","publication_status":"published","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Redig, Frank","last_name":"Redig","first_name":"Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"first_name":"Federico","last_name":"Sau","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"oa":1,"volume":25,"intvolume":"        25","arxiv":1,"publication":"Electronic Journal of Probability","date_updated":"2023-10-17T12:51:56Z","ec_funded":1,"department":[{"_id":"JaMa"}],"article_type":"original","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","publication_identifier":{"eissn":["1083-6489"]},"doi":"10.1214/20-EJP536","scopus_import":"1","file_date_updated":"2020-12-28T08:24:08Z","article_processing_charge":"No","oa_version":"Published Version","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","publication_status":"published","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"year":"2020","article_number":"138","citation":{"chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>.","apa":"Redig, F., Saada, E., &#38; Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>, vol. 25, 138,  Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” <i>Electronic Journal of Probability</i>, vol. 25.  Institute of Mathematical Statistics, 2020."},"_id":"8973","date_created":"2020-12-27T23:01:17Z","file":[{"date_updated":"2020-12-28T08:24:08Z","relation":"main_file","date_created":"2020-12-28T08:24:08Z","file_size":696653,"access_level":"open_access","success":1,"file_name":"2020_ElectronJProbab_Redig.pdf","checksum":"d75359b9814e78d57c0a481b7cde3751","file_id":"8976","creator":"dernst","content_type":"application/pdf"}],"publisher":" Institute of Mathematical Statistics","date_published":"2020-10-21T00:00:00Z","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["510"],"status":"public","month":"10","isi":1,"day":"21","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1"},{"day":"18","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"project":[{"grant_number":"T0101031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"}],"has_accepted_license":"1","issue":"3","publisher":"Elsevier","pmid":1,"external_id":{"pmid":["33377108"]},"date_published":"2020-12-18T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"status":"public","month":"12","article_type":"original","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publication_identifier":{"issn":["2666-1667"]},"doi":"10.1016/j.xpro.2020.100215","file_date_updated":"2021-01-07T15:57:27Z","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).","lang":"eng"}],"article_number":"100215","year":"2020","citation":{"short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>.","apa":"Laukoter, S., Amberg, N., Pauler, F., &#38; Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>","mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>, vol. 1, no. 3, 100215, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>.","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215.","ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” <i>STAR Protocols</i>, vol. 1, no. 3. Elsevier, 2020.","ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>"},"_id":"8978","file":[{"checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","content_type":"application/pdf","file_id":"8996","creator":"dernst","relation":"main_file","date_updated":"2021-01-07T15:57:27Z","date_created":"2021-01-07T15:57:27Z","file_size":4031449,"file_name":"2020_STARProtocols_Laukoter.pdf","success":1,"access_level":"open_access"}],"date_created":"2020-12-30T10:17:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Laukoter","first_name":"Susanne","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"oa":1,"volume":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":"         1","publication":"STAR Protocols","date_updated":"2021-01-12T08:21:36Z","ec_funded":1,"department":[{"_id":"SiHi"}]},{"type":"dissertation","date_published":"2020-12-30T00:00:00Z","publisher":"Institute of Science and Technology Austria","month":"12","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"page":"141","day":"30","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8557"},{"relation":"part_of_dissertation","status":"public","id":"6187"}]},"author":[{"last_name":"Emtenani","first_name":"Shamsi","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaSi"}],"date_updated":"2023-09-07T13:24:17Z","degree_awarded":"PhD","publication_status":"published","title":"Metabolic regulation of Drosophila macrophage tissue invasion","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-12-31T23:30:04Z","doi":"10.15479/AT:ISTA:8983","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","file":[{"checksum":"ec2797ab7a6f253b35df0572b36d1b43","content_type":"application/pdf","file_id":"8984","creator":"semtenan","embargo":"2021-12-30","date_updated":"2021-12-31T23:30:04Z","date_created":"2020-12-30T15:34:01Z","file_size":10848175,"relation":"main_file","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","access_level":"open_access"},{"content_type":"application/pdf","creator":"semtenan","file_id":"8985","checksum":"cc30e6608a9815414024cf548dff3b3a","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","access_level":"closed","date_updated":"2021-12-31T23:30:04Z","file_size":10073648,"date_created":"2020-12-30T15:37:36Z","embargo_to":"open_access","relation":"source_file"}],"date_created":"2020-12-30T15:41:26Z","_id":"8983","citation":{"mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>.","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>"},"year":"2020","supervisor":[{"last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}]},{"day":"11","quality_controlled":"1","issue":"50","license":"https://creativecommons.org/licenses/by-nc/4.0/","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"pmid":1,"publisher":"AAAS","type":"journal_article","external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"date_published":"2020-12-11T00:00:00Z","ddc":["580"],"language":[{"iso":"eng"}],"isi":1,"month":"12","status":"public","scopus_import":"1","doi":"10.1126/sciadv.abc8895","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","publication_identifier":{"eissn":["2375-2548"]},"article_type":"original","publication_status":"published","title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-01-07T12:44:33Z","citation":{"ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” <i>Science Advances</i>, vol. 6, no. 50. AAAS, 2020.","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. 2020;6(50). doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., &#38; Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>."},"article_number":"eabc8895","year":"2020","abstract":[{"lang":"eng","text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants."}],"date_created":"2021-01-03T23:01:23Z","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"8994","checksum":"5ac2500b191c08ef6dab5327f40ff663","access_level":"open_access","success":1,"file_name":"2020_ScienceAdvances_Zhang.pdf","file_size":10578145,"relation":"main_file","date_created":"2021-01-07T12:44:33Z","date_updated":"2021-01-07T12:44:33Z"}],"_id":"8986","author":[{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":6,"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"intvolume":"         6","department":[{"_id":"JiFr"}],"date_updated":"2024-10-29T10:22:43Z","ec_funded":1,"publication":"Science Advances"},{"project":[{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"day":"08","page":"3-15","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12","publisher":"Springer Nature","type":"conference","date_published":"2020-12-08T00:00:00Z","external_id":{"isi":["000927592800001"]},"abstract":[{"lang":"eng","text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message."}],"citation":{"ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: <i>Progress in Cryptology</i>. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in <i>Progress in Cryptology</i>, Bangalore, India, 2020, vol. 12578, pp. 3–15.","short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In <i>Progress in Cryptology</i>, 12578:3–15. LNCS. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>.","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In <i>Progress in Cryptology</i> (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” <i>Progress in Cryptology</i>, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>."},"year":"2020","date_created":"2021-01-03T23:01:23Z","_id":"8987","conference":{"end_date":"2020-12-16","name":"INDOCRYPT: International Conference on Cryptology in India","location":"Bangalore, India","start_date":"2020-12-13"},"publication_identifier":{"isbn":["9783030652760"],"eissn":["16113349"],"issn":["03029743"]},"scopus_import":"1","doi":"10.1007/978-3-030-65277-7_1","main_file_link":[{"url":"https://eprint.iacr.org/2020/418","open_access":"1"}],"article_processing_charge":"No","oa_version":"Preprint","title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","publication_status":"published","intvolume":"     12578","ec_funded":1,"date_updated":"2023-08-24T11:08:58Z","publication":"Progress in Cryptology","department":[{"_id":"KrPi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"volume":12578,"oa":1,"series_title":"LNCS"},{"date_published":"2020-12-15T00:00:00Z","external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"type":"journal_article","publisher":"National Academy of Sciences","pmid":1,"month":"12","isi":1,"status":"public","language":[{"iso":"eng"}],"ddc":["570"],"quality_controlled":"1","page":"31614-31622","day":"15","issue":"50","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/","relation":"press_release","description":"News on IST Homepage"}]},"oa":1,"volume":117,"author":[{"last_name":"Grah","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GaTk"}],"publication":"PNAS","date_updated":"2023-08-24T11:10:22Z","intvolume":"       117","publication_status":"published","title":"Nonequilibrium models of optimal enhancer function","file_date_updated":"2021-01-11T08:37:31Z","article_processing_charge":"No","oa_version":"Published Version","doi":"10.1073/pnas.2006731117","scopus_import":"1","article_type":"original","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"_id":"9000","file":[{"checksum":"69039cd402a571983aa6cb4815ffa863","file_id":"9004","creator":"dernst","content_type":"application/pdf","date_created":"2021-01-11T08:37:31Z","date_updated":"2021-01-11T08:37:31Z","file_size":1199247,"relation":"main_file","file_name":"2020_PNAS_Grah.pdf","access_level":"open_access","success":1}],"date_created":"2021-01-10T23:01:17Z","year":"2020","citation":{"ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>PNAS</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>."},"abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}]},{"author":[{"last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefano","last_name":"Pirandola","full_name":"Pirandola, Stefano"},{"full_name":"Vitali, David","first_name":"David","last_name":"Vitali"},{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":2020,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7910"}]},"oa":1,"arxiv":1,"intvolume":"      2020","department":[{"_id":"JoFi"}],"date_updated":"2024-09-10T12:23:52Z","ec_funded":1,"publication":"IEEE National Radar Conference - Proceedings","scopus_import":"1","doi":"10.1109/RadarConf2043947.2020.9266397","main_file_link":[{"url":"https://arxiv.org/abs/1908.03058","open_access":"1"}],"acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie Skłodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","publication_identifier":{"isbn":["9781728189420"],"issn":["1097-5659"]},"publication_status":"published","title":"Microwave quantum illumination with a digital phase-conjugated receiver","article_processing_charge":"No","oa_version":"Preprint","citation":{"ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in <i>IEEE National Radar Conference - Proceedings</i>, Florence, Italy, 2020, vol. 2020, no. 9.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: <i>IEEE National Radar Conference - Proceedings</i>. Vol 2020. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., &#38; Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In <i>IEEE National Radar Conference - Proceedings</i> (Vol. 2020). Florence, Italy: IEEE. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>","chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In <i>IEEE National Radar Conference - Proceedings</i>, Vol. 2020. IEEE, 2020. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” <i>IEEE National Radar Conference - Proceedings</i>, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>."},"year":"2020","article_number":"9266397","abstract":[{"lang":"eng","text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits."}],"conference":{"start_date":"2020-09-21","location":"Florence, Italy","name":"RadarConf: National Conference on Radar","end_date":"2020-09-25"},"date_created":"2021-01-10T23:01:17Z","_id":"9001","publisher":"IEEE","type":"conference","external_id":{"arxiv":["1908.03058"],"isi":["000612224900089"]},"date_published":"2020-09-21T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"month":"09","status":"public","day":"21","quality_controlled":"1","issue":"9","project":[{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894","call_identifier":"H2020"}]},{"_id":"9007","date_created":"2021-01-17T23:01:11Z","abstract":[{"lang":"eng","text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals."}],"year":"2020","citation":{"ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. 2020;95(4):635-659. doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society, 2020. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>.","apa":"Browning, T. D., &#38; Sawin, W. (2020). Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>."},"oa_version":"Preprint","article_processing_charge":"No","title":"Free rational points on smooth hypersurfaces","publication_status":"published","article_type":"original","publication_identifier":{"issn":["00102571"],"eissn":["14208946"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08463"}],"doi":"10.4171/CMH/499","scopus_import":"1","publication":"Commentarii Mathematici Helvetici","date_updated":"2023-08-24T11:11:36Z","department":[{"_id":"TiBr"}],"intvolume":"        95","arxiv":1,"oa":1,"volume":95,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"issue":"4","quality_controlled":"1","day":"07","page":"635-659","status":"public","month":"12","isi":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"date_published":"2020-12-07T00:00:00Z","type":"journal_article","publisher":"European Mathematical Society"},{"acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-Ramón Troncoso Pastoriza, Frédéric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","publication_identifier":{"eissn":["2150-8097"]},"article_type":"original","scopus_import":"1","doi":"10.14778/3436905.3436917","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.14778/3436905.3436917"}],"oa_version":"Published Version","article_processing_charge":"No","title":"CALYPSO: Private data management for decentralized ledgers","publication_status":"published","abstract":[{"lang":"eng","text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees."}],"citation":{"mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>.","short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599.","chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>.","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., &#38; Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020.","ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599.","ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. 2020;14(4):586-599. doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>"},"year":"2020","date_created":"2021-01-17T23:01:13Z","_id":"9011","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Enis Ceyhun","last_name":"Alp","full_name":"Alp, Enis Ceyhun"},{"full_name":"Gasser, Linus","last_name":"Gasser","first_name":"Linus"},{"last_name":"Jovanovic","first_name":"Philipp","full_name":"Jovanovic, Philipp"},{"first_name":"Ewa","last_name":"Syta","full_name":"Syta, Ewa"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"volume":14,"oa":1,"intvolume":"        14","date_updated":"2023-08-24T13:57:13Z","publication":"Proceedings of the VLDB Endowment","department":[{"_id":"ElKo"}],"day":"01","page":"586-599","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"4","publisher":"Association for Computing Machinery","type":"journal_article","external_id":{"isi":["000658495400012"]},"date_published":"2020-12-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12"},{"ddc":["510"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","external_id":{"isi":["000600695200027"]},"date_published":"2020-12-15T00:00:00Z","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"6","day":"15","page":"6222-6233","quality_controlled":"1","intvolume":"        52","ec_funded":1,"date_updated":"2023-08-24T11:15:16Z","publication":"SIAM Journal on Mathematical Analysis","department":[{"_id":"JuFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"},{"full_name":"Simon, Theresa M.","first_name":"Theresa M.","last_name":"Simon"}],"volume":52,"oa":1,"abstract":[{"text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems.","lang":"eng"}],"citation":{"mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>.","apa":"Fischer, J. L., Laux, T., &#38; Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233.","chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>.","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(6):6222-6233. doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>"},"year":"2020","file":[{"date_created":"2021-01-25T07:48:39Z","date_updated":"2021-01-25T07:48:39Z","relation":"main_file","file_size":310655,"success":1,"access_level":"open_access","file_name":"2020_SIAM_Fischer.pdf","checksum":"21aa1cf4c30a86a00cae15a984819b5d","content_type":"application/pdf","creator":"dernst","file_id":"9041"}],"date_created":"2021-01-24T23:01:09Z","_id":"9039","publication_identifier":{"eissn":["10957154"],"issn":["00361410"]},"acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","article_type":"original","scopus_import":"1","doi":"10.1137/20M1322182","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-01-25T07:48:39Z","publication_status":"published","title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Par Alizadeh","last_name":"Alamdari","full_name":"Alamdari, Par Alizadeh"},{"last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lukina","first_name":"Anna","full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"}],"oa":1,"date_updated":"2021-02-09T09:39:59Z","publication":"Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design","department":[{"_id":"ToHe"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publication_identifier":{"eissn":["2708-7824"],"isbn":["9783854480426"]},"scopus_import":"1","doi":"10.34727/2020/isbn.978-3-85448-042-6_21","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-02-09T09:39:02Z","publication_status":"published","title":"Formal methods with a touch of magic","abstract":[{"text":"Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.","lang":"eng"}],"citation":{"ista":"Alamdari PA, Avni G, Henzinger TA, Lukina A. 2020. Formal methods with a touch of magic. Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design.  FMCAD: Formal Methods in Computer-Aided Design, 138–147.","ieee":"P. A. Alamdari, G. Avni, T. A. Henzinger, and A. Lukina, “Formal methods with a touch of magic,” in <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, Online Conference, 2020, pp. 138–147.","ama":"Alamdari PA, Avni G, Henzinger TA, Lukina A. Formal methods with a touch of magic. In: <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>. TU Wien Academic Press; 2020:138-147. doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>","chicago":"Alamdari, Par Alizadeh, Guy Avni, Thomas A Henzinger, and Anna Lukina. “Formal Methods with a Touch of Magic.” In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, 138–47. TU Wien Academic Press, 2020. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>.","apa":"Alamdari, P. A., Avni, G., Henzinger, T. A., &#38; Lukina, A. (2020). Formal methods with a touch of magic. In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i> (pp. 138–147). Online Conference: TU Wien Academic Press. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>","short":"P.A. Alamdari, G. Avni, T.A. Henzinger, A. Lukina, in:, Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–147.","mla":"Alamdari, Par Alizadeh, et al. “Formal Methods with a Touch of Magic.” <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, TU Wien Academic Press, 2020, pp. 138–47, doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>."},"year":"2020","file":[{"checksum":"d616d549a0ade78606b16f8a9540820f","content_type":"application/pdf","file_id":"9109","creator":"dernst","date_created":"2021-02-09T09:39:02Z","file_size":990999,"date_updated":"2021-02-09T09:39:02Z","relation":"main_file","file_name":"2020_FMCAD_Alamdari.pdf","access_level":"open_access","success":1}],"date_created":"2021-01-24T23:01:10Z","_id":"9040","conference":{"start_date":"2020-09-21","name":" FMCAD: Formal Methods in Computer-Aided Design","location":"Online Conference","end_date":"2020-09-24"},"publisher":"TU Wien Academic Press","type":"conference","date_published":"2020-09-21T00:00:00Z","ddc":["000"],"language":[{"iso":"eng"}],"status":"public","month":"09","day":"21","page":"138-147","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}]}]