[{"language":[{"iso":"eng"}],"date_updated":"2023-08-21T06:26:50Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:04Z","title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","doi":"10.7554/eLife.56839","tmp":{"short":"CC BY (4.0)","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"},"article_number":"e56839","citation":{"ieee":"J. Bao <i>et al.</i>, “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","ista":"Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.","ama":"Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>","mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>, vol. 9, e56839, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>.","chicago":"Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>.","apa":"Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>"},"month":"05","oa":1,"ddc":["570"],"publication":"eLife","isi":1,"pmid":1,"publication_status":"published","day":"13","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-05-13T00:00:00Z","status":"public","has_accepted_license":"1","author":[{"full_name":"Bao, Jin","first_name":"Jin","last_name":"Bao"},{"full_name":"Graupner, Michael","first_name":"Michael","last_name":"Graupner"},{"last_name":"Astorga","first_name":"Guadalupe","full_name":"Astorga, Guadalupe"},{"full_name":"Collin, Thibault","first_name":"Thibault","last_name":"Collin"},{"last_name":"Jalil","first_name":"Abdelali","full_name":"Jalil, Abdelali"},{"full_name":"Indriati, Dwi Wahyu","last_name":"Indriati","first_name":"Dwi Wahyu"},{"full_name":"Bradley, Jonathan","last_name":"Bradley","first_name":"Jonathan"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"},{"first_name":"Isabel","last_name":"Llano","full_name":"Llano, Isabel"}],"article_type":"original","file":[{"file_id":"7891","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":4832050,"checksum":"8ea99bb6660cc407dbdb00c173b01683","access_level":"open_access","date_created":"2020-05-26T09:34:54Z","file_name":"2020_eLife_Bao.pdf","relation":"main_file"}],"article_processing_charge":"No","_id":"7878","intvolume":"         9","abstract":[{"lang":"eng","text":"Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions."}],"license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"year":"2020","type":"journal_article","volume":9,"date_created":"2020-05-24T22:00:58Z","oa_version":"Published Version","publication_identifier":{"eissn":["2050084X"]}},{"date_updated":"2023-08-21T06:26:22Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1074/jbc.RA120.012628","title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","citation":{"ieee":"R. R. Fagan <i>et al.</i>, “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","short":"R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244.","ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. 2020;295(16):5229-5244. doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>","mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>.","ista":"Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.","chicago":"Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>. ASBMB Publications, 2020. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>.","apa":"Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. ASBMB Publications. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>"},"main_file_link":[{"url":"https://escholarship.umassmed.edu/oapubs/4187","open_access":"1"}],"publication":"Journal of Biological Chemistry","isi":1,"oa":1,"month":"04","day":"17","publication_status":"published","issue":"16","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SaSi"}],"publisher":"ASBMB Publications","date_published":"2020-04-17T00:00:00Z","status":"public","article_type":"original","author":[{"full_name":"Fagan, Rita R.","last_name":"Fagan","first_name":"Rita R."},{"first_name":"Patrick J.","last_name":"Kearney","full_name":"Kearney, Patrick J."},{"first_name":"Carolyn G.","last_name":"Sweeney","full_name":"Sweeney, Carolyn G."},{"full_name":"Luethi, Dino","last_name":"Luethi","first_name":"Dino"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"full_name":"Schicker, Klaus","last_name":"Schicker","first_name":"Klaus"},{"full_name":"Alejandro, Brian S.","first_name":"Brian S.","last_name":"Alejandro"},{"last_name":"O'Connor","first_name":"Lauren C.","full_name":"O'Connor, Lauren C."},{"last_name":"Sitte","first_name":"Harald H.","full_name":"Sitte, Harald H."},{"last_name":"Melikian","first_name":"Haley E.","full_name":"Melikian, Haley E."}],"article_processing_charge":"No","_id":"7880","intvolume":"       295","page":"5229-5244","scopus_import":"1","abstract":[{"text":"Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. ","lang":"eng"}],"year":"2020","external_id":{"pmid":["32132171"],"isi":["000530288000006"]},"volume":295,"date_created":"2020-05-24T22:00:59Z","type":"journal_article","publication_identifier":{"eissn":["1083351X"],"issn":["00219258"]},"oa_version":"Submitted Version"},{"article_processing_charge":"No","_id":"7882","intvolume":"         8","article_type":"original","author":[{"last_name":"Armstrong","first_name":"Jeremy R.","full_name":"Armstrong, Jeremy R."},{"full_name":"Jensen, Aksel S.","last_name":"Jensen","first_name":"Aksel S."},{"last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zinner","first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T."}],"ec_funded":1,"file":[{"file_name":"2020_Mathematics_Armstrong.pdf","relation":"main_file","date_created":"2020-05-25T14:42:22Z","access_level":"open_access","checksum":"a05a7df724522203d079673a0d4de4bc","date_updated":"2020-07-14T12:48:04Z","file_size":990540,"creator":"dernst","content_type":"application/pdf","file_id":"7887"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-24T22:01:00Z","volume":8,"type":"journal_article","publication_identifier":{"eissn":["22277390"]},"oa_version":"Published Version","scopus_import":"1","abstract":[{"text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes.","lang":"eng"}],"year":"2020","external_id":{"isi":["000531824100024"]},"tmp":{"short":"CC BY (4.0)","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"},"doi":"10.3390/math8040484","title":"Clusters in separated tubes of tilted dipoles","article_number":"484","citation":{"ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” <i>Mathematics</i>, vol. 8, no. 4. MDPI, 2020.","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. 2020;8(4). doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>, vol. 8, no. 4, 484, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., &#38; Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>","chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>."},"language":[{"iso":"eng"}],"date_updated":"2023-08-21T06:23:36Z","file_date_updated":"2020-07-14T12:48:04Z","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"publisher":"MDPI","has_accepted_license":"1","status":"public","date_published":"2020-04-01T00:00:00Z","publication":"Mathematics","isi":1,"ddc":["510"],"oa":1,"month":"04","day":"01","publication_status":"published","issue":"4"},{"publication_status":"published","day":"25","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/"}],"record":[{"id":"14697","relation":"dissertation_contains","status":"public"},{"status":"public","id":"12401","relation":"dissertation_contains"}]},"publication":"Nature","isi":1,"month":"06","date_published":"2020-06-25T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","quality_controlled":"1","date_updated":"2024-03-25T23:30:12Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"citation":{"short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. <i>Nature</i>. 2020;582:582–585. doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>, vol. 582, Springer Nature, 2020, pp. 582–585, doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>","ieee":"A. Reversat <i>et al.</i>, “Cellular locomotion using environmental topography,” <i>Nature</i>, vol. 582. Springer Nature, pp. 582–585, 2020."},"doi":"10.1038/s41586-020-2283-z","title":"Cellular locomotion using environmental topography","year":"2020","external_id":{"isi":["000532688300008"]},"page":"582–585","scopus_import":"1","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"oa_version":"None","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29911","call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-24T22:01:01Z","volume":582,"type":"journal_article","article_type":"original","ec_funded":1,"author":[{"first_name":"Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"first_name":"Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"last_name":"Tasciyan","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L"},{"last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miroslav","last_name":"Hons","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav"},{"full_name":"Piel, Matthieu","first_name":"Matthieu","last_name":"Piel"},{"first_name":"Andrew","last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew"},{"first_name":"Raphael","last_name":"Voituriez","full_name":"Voituriez, Raphael"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"intvolume":"       582","article_processing_charge":"No","_id":"7885"},{"publication_identifier":{"issn":["2050-084X"]},"oa_version":"Published Version","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"volume":9,"date_created":"2020-05-25T15:01:40Z","type":"journal_article","year":"2020","external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"scopus_import":"1","abstract":[{"text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.","lang":"eng"}],"intvolume":"         9","article_processing_charge":"No","_id":"7888","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"7890","checksum":"f6aad884cf706846ae9357fcd728f8b5","file_size":7744848,"date_updated":"2020-07-14T12:48:04Z","access_level":"open_access","relation":"main_file","file_name":"2020_eLife_Schauer.pdf","date_created":"2020-05-25T15:15:43Z"}],"article_type":"original","ec_funded":1,"author":[{"orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer"},{"full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro","first_name":"Diana C"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"has_accepted_license":"1","date_published":"2020-04-06T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"},{"_id":"Bio"}],"day":"06","publication_status":"published","related_material":{"record":[{"status":"public","id":"12891","relation":"dissertation_contains"}]},"pmid":1,"isi":1,"publication":"eLife","ddc":["570"],"oa":1,"month":"04","citation":{"chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., &#38; Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>, vol. 9, e55190, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>.","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"article_number":"e55190","tmp":{"short":"CC BY (4.0)","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"},"doi":"10.7554/elife.55190","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","file_date_updated":"2020-07-14T12:48:04Z","quality_controlled":"1","date_updated":"2023-08-21T06:25:49Z","language":[{"iso":"eng"}]},{"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"}],"type":"journal_article","date_created":"2020-05-25T15:02:00Z","volume":38,"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"oa_version":"Submitted Version","scopus_import":"1","page":"944-946","abstract":[{"lang":"eng","text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants."}],"external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"year":"2020","_id":"7889","article_processing_charge":"No","intvolume":"        38","ec_funded":1,"author":[{"last_name":"Mitiouchkina","first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer","first_name":"Louisa"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"first_name":"Tatiana V.","last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V."},{"full_name":"Guglya, Elena B.","first_name":"Elena B.","last_name":"Guglya"},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"first_name":"Kseniia A.","last_name":"Palkina","full_name":"Palkina, Kseniia A."},{"full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S.","last_name":"Shakhova"},{"last_name":"Fakhranurova","first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I."},{"first_name":"Sofia V.","last_name":"Chekova","full_name":"Chekova, Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S.","last_name":"Tsarkova"},{"first_name":"Yaroslav V.","last_name":"Golubev","full_name":"Golubev, Yaroslav V."},{"first_name":"Vadim V.","last_name":"Negrebetsky","full_name":"Negrebetsky, Vadim V."},{"full_name":"Dolgushin, Sergey A.","last_name":"Dolgushin","first_name":"Sergey A."},{"last_name":"Shalaev","first_name":"Pavel V.","full_name":"Shalaev, Pavel V."},{"full_name":"Shlykov, Dmitry","first_name":"Dmitry","last_name":"Shlykov"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"first_name":"Sergey M.","last_name":"Deyev","full_name":"Deyev, Sergey M."},{"first_name":"Andrey I.","last_name":"Bubyrev","full_name":"Bubyrev, Andrey I."},{"full_name":"Pushin, Alexander S.","first_name":"Alexander S.","last_name":"Pushin"},{"last_name":"Choob","first_name":"Vladimir V.","full_name":"Choob, Vladimir V."},{"full_name":"Dolgov, Sergey V.","first_name":"Sergey V.","last_name":"Dolgov"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Yampolsky","first_name":"Ilia V.","full_name":"Yampolsky, Ilia V."},{"last_name":"Sarkisyan","first_name":"Karen S.","full_name":"Sarkisyan, Karen S."}],"article_type":"original","file":[{"date_created":"2020-08-28T08:57:07Z","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-03-02T23:30:03Z","file_size":1180086,"checksum":"1b30467500ec6277229a875b06e196d0","embargo":"2021-03-01","file_id":"8316","creator":"dernst","content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"has_accepted_license":"1","status":"public","date_published":"2020-04-27T00:00:00Z","ddc":["570"],"isi":1,"publication":"Nature Biotechnology","month":"04","oa":1,"publication_status":"published","day":"27","pmid":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"title":"Plants with genetically encoded autoluminescence","doi":"10.1038/s41587-020-0500-9","citation":{"ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. 2020;38:944-946. doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>, vol. 38, Springer Nature, 2020, pp. 944–46, doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>."},"language":[{"iso":"eng"}],"date_updated":"2023-09-05T15:30:34Z","quality_controlled":"1","file_date_updated":"2021-03-02T23:30:03Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"has_accepted_license":"1","supervisor":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_published":"2020-05-25T00:00:00Z","status":"public","ddc":["000"],"month":"05","oa":1,"publication_status":"published","day":"25","related_material":{"record":[{"relation":"part_of_dissertation","id":"6677","status":"public"}]},"tmp":{"short":"CC BY (4.0)","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"},"title":"On the average-case hardness of total search problems","doi":"10.15479/AT:ISTA:7896","citation":{"short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","mla":"Kamath Hosdurg, Chethan. <i>On the Average-Case Hardness of Total Search Problems</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7896\">10.15479/AT:ISTA:7896</a>.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7896\">10.15479/AT:ISTA:7896</a>","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7896\">https://doi.org/10.15479/AT:ISTA:7896</a>.","apa":"Kamath Hosdurg, C. (2020). <i>On the average-case hardness of total search problems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7896\">https://doi.org/10.15479/AT:ISTA:7896</a>","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020."},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:15:55Z","file_date_updated":"2020-07-14T12:48:04Z","project":[{"grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"type":"dissertation","degree_awarded":"PhD","date_created":"2020-05-26T14:08:55Z","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","page":"126","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"year":"2020","_id":"7896","article_processing_charge":"No","ec_funded":1,"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"}],"file":[{"access_level":"open_access","date_created":"2020-05-26T14:08:13Z","relation":"main_file","file_name":"2020_Thesis_Kamath.pdf","file_id":"7897","creator":"dernst","content_type":"application/pdf","file_size":1622742,"date_updated":"2020-07-14T12:48:04Z","checksum":"b39e2e1c376f5819b823fb7077491c64"},{"access_level":"closed","relation":"source_file","file_name":"Thesis_Kamath.zip","date_created":"2020-05-26T14:08:23Z","content_type":"application/x-zip-compressed","file_id":"7898","creator":"dernst","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","file_size":15301529,"date_updated":"2020-07-14T12:48:04Z"}]},{"ec_funded":1,"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras"}],"file":[{"file_name":"PhDThesis_Contreras.docx","relation":"source_file","date_created":"2020-06-05T08:18:08Z","access_level":"closed","checksum":"43c172bf006c95b65992d473c7240d13","date_updated":"2021-06-07T22:30:03Z","embargo_to":"open_access","file_size":53134142,"file_id":"7927","creator":"xcontreras","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"content_type":"application/pdf","creator":"xcontreras","file_id":"7928","embargo":"2021-06-06","file_size":35117191,"date_updated":"2021-06-07T22:30:03Z","checksum":"addfed9128271be05cae3608e03a6ec0","access_level":"open_access","date_created":"2020-06-05T08:18:07Z","relation":"main_file","file_name":"PhDThesis_Contreras.pdf"}],"_id":"7902","article_processing_charge":"No","page":"214","abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"year":"2020","project":[{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-29T08:27:32Z","degree_awarded":"PhD","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2023-10-18T08:45:16Z","file_date_updated":"2021-06-07T22:30:03Z","doi":"10.15479/AT:ISTA:7902","title":"Genetic dissection of neural development in health and disease at single cell resolution","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"citation":{"ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). <i>Genetic dissection of neural development in health and disease at single cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>","mla":"Contreras, Ximena. <i>Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020."},"alternative_title":["ISTA Thesis"],"ddc":["570"],"oa":1,"month":"06","day":"05","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"6830","status":"public"},{"status":"public","id":"28","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"7815","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","date_published":"2020-06-05T00:00:00Z","supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}]},{"file":[{"file_name":"2020_JourNeuroscience_Wang.pdf","relation":"main_file","date_created":"2020-06-02T09:12:16Z","access_level":"open_access","checksum":"6571607ea9036154b67cc78e848a7f7d","date_updated":"2020-07-14T12:48:05Z","file_size":3817360,"creator":"dernst","content_type":"application/pdf","file_id":"7912"}],"article_type":"original","author":[{"first_name":"Han Ying","last_name":"Wang","full_name":"Wang, Han Ying"},{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi"},{"last_name":"Yamashita","first_name":"Takayuki","full_name":"Yamashita, Takayuki"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"intvolume":"        40","_id":"7908","article_processing_charge":"No","year":"2020","external_id":{"isi":["000535694700004"]},"scopus_import":"1","page":"4103-4115","abstract":[{"lang":"eng","text":"Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses."}],"publication_identifier":{"eissn":["15292401"]},"oa_version":"Published Version","volume":40,"date_created":"2020-05-31T22:00:48Z","type":"journal_article","file_date_updated":"2020-07-14T12:48:05Z","quality_controlled":"1","date_updated":"2023-08-21T06:31:25Z","language":[{"iso":"eng"}],"citation":{"ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” <i>Journal of Neuroscience</i>, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020.","ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. 2020;40(21):4103-4115. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>.","ista":"Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115.","short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., &#38; Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>","chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>."},"tmp":{"short":"CC BY (4.0)","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"},"doi":"10.1523/JNEUROSCI.2946-19.2020","title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","publication_status":"published","day":"20","issue":"21","publication":"Journal of Neuroscience","isi":1,"ddc":["570"],"oa":1,"month":"05","has_accepted_license":"1","date_published":"2020-05-20T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"publisher":"Society for Neuroscience"},{"doi":"10.7554/eLife.55351","title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","tmp":{"short":"CC BY (4.0)","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"},"article_number":"e55351","citation":{"short":"J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020).","ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>","mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>, vol. 9, e55351, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>.","ista":"Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351.","chicago":"Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>.","apa":"Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>","ieee":"J. Damiano-Guercio <i>et al.</i>, “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"language":[{"iso":"eng"}],"date_updated":"2023-08-21T06:32:25Z","file_date_updated":"2020-07-14T12:48:05Z","quality_controlled":"1","publisher":"eLife Sciences Publications","department":[{"_id":"MiSi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2020-05-11T00:00:00Z","has_accepted_license":"1","oa":1,"month":"05","isi":1,"publication":"eLife","ddc":["570"],"publication_status":"published","day":"11","_id":"7909","article_processing_charge":"No","intvolume":"         9","article_type":"original","author":[{"full_name":"Damiano-Guercio, Julia","last_name":"Damiano-Guercio","first_name":"Julia"},{"full_name":"Kurzawa, Laëtitia","last_name":"Kurzawa","first_name":"Laëtitia"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","first_name":"Jan"},{"first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"full_name":"Schaks, Matthias","first_name":"Matthias","last_name":"Schaks"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","first_name":"Maria"},{"full_name":"Pokrant, Thomas","first_name":"Thomas","last_name":"Pokrant"},{"full_name":"Brühmann, Stefan","first_name":"Stefan","last_name":"Brühmann"},{"last_name":"Linkner","first_name":"Joern","full_name":"Linkner, Joern"},{"first_name":"Laurent","last_name":"Blanchoin","full_name":"Blanchoin, Laurent"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"}],"ec_funded":1,"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"7914","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","file_size":10535713,"date_updated":"2020-07-14T12:48:05Z","access_level":"open_access","relation":"main_file","file_name":"2020_eLife_Damiano_Guercio.pdf","date_created":"2020-06-02T10:35:37Z"}],"volume":9,"date_created":"2020-05-31T22:00:49Z","type":"journal_article","project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2050084X"]},"abstract":[{"text":"Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.","lang":"eng"}],"scopus_import":"1","year":"2020","external_id":{"isi":["000537208000001"]}},{"language":[{"iso":"eng"}],"date_updated":"2024-09-10T12:23:52Z","file_date_updated":"2020-07-14T12:48:05Z","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","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"},"title":"Microwave quantum illumination using a digital receiver","doi":"10.1126/sciadv.abb0451","article_number":"eabb0451","citation":{"ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination using a digital receiver. Science Advances. 6(19), eabb0451.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination using a digital receiver. <i>Science Advances</i>. 2020;6(19). doi:<a href=\"https://doi.org/10.1126/sciadv.abb0451\">10.1126/sciadv.abb0451</a>","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination Using a Digital Receiver.” <i>Science Advances</i>, vol. 6, no. 19, eabb0451, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abb0451\">10.1126/sciadv.abb0451</a>.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, Science Advances 6 (2020).","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., &#38; Fink, J. M. (2020). Microwave quantum illumination using a digital receiver. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abb0451\">https://doi.org/10.1126/sciadv.abb0451</a>","chicago":"Barzanjeh, Shabir, S. Pirandola, D Vitali, and Johannes M Fink. “Microwave Quantum Illumination Using a Digital Receiver.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abb0451\">https://doi.org/10.1126/sciadv.abb0451</a>.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination using a digital receiver,” <i>Science Advances</i>, vol. 6, no. 19. AAAS, 2020."},"ddc":["530"],"isi":1,"publication":"Science Advances","month":"05","oa":1,"day":"06","publication_status":"published","issue":"19","related_material":{"record":[{"id":"9001","relation":"later_version","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/scientists-demonstrate-quantum-radar-prototype/"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoFi"}],"publisher":"AAAS","has_accepted_license":"1","date_published":"2020-05-06T00:00:00Z","status":"public","ec_funded":1,"author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh"},{"last_name":"Pirandola","first_name":"S.","full_name":"Pirandola, S."},{"full_name":"Vitali, D","last_name":"Vitali","first_name":"D"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"article_type":"original","file":[{"date_created":"2020-06-02T09:18:36Z","relation":"main_file","file_name":"2020_ScienceAdvances_Barzanjeh.pdf","access_level":"open_access","file_size":795822,"date_updated":"2020-07-14T12:48:05Z","checksum":"16fa61cc1951b444ee74c07188cda9da","file_id":"7913","content_type":"application/pdf","creator":"dernst"}],"_id":"7910","article_processing_charge":"No","intvolume":"         6","scopus_import":"1","abstract":[{"text":"Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"external_id":{"arxiv":["1908.03058"],"isi":["000531171100045"]},"year":"2020","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020"},{"name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","date_created":"2020-05-31T22:00:49Z","volume":6,"arxiv":1,"publication_identifier":{"eissn":["23752548"]},"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"We explore the time evolution of two impurities in a trapped one-dimensional Bose gas that follows a change of the boson-impurity interaction. We study the induced impurity-impurity interactions and their effect on the quench dynamics. In particular, we report on the size of the impurity cloud, the impurity-impurity entanglement, and the impurity-impurity correlation function. The presented numerical simulations are based upon the variational multilayer multiconfiguration time-dependent Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations, we employ an effective two-body Hamiltonian with a contact interaction. We show that the effective model consistent with the mean-field attraction of two heavy impurities explains qualitatively our results for weak interactions. Our findings suggest that the quench dynamics in cold-atom systems can be a tool for studying impurity-impurity correlations."}],"year":"2020","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"volume":2,"date_created":"2020-06-03T11:30:10Z","type":"journal_article","publication_identifier":{"issn":["2643-1564"]},"oa_version":"Published Version","article_type":"original","ec_funded":1,"author":[{"first_name":"S. I.","last_name":"Mistakidis","full_name":"Mistakidis, S. I."},{"last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."}],"file":[{"content_type":"application/pdf","file_id":"7926","creator":"dernst","checksum":"e1c362fe094d6b246b3cd4a49722e78b","date_updated":"2020-07-14T12:48:05Z","file_size":1741098,"access_level":"open_access","file_name":"2020_PhysRevResearch_Mistakidis.pdf","relation":"main_file","date_created":"2020-06-04T13:51:59Z"}],"article_processing_charge":"No","_id":"7919","intvolume":"         2","publication":"Physical Review Research","ddc":["530"],"oa":1,"month":"05","day":"11","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"has_accepted_license":"1","status":"public","date_published":"2020-05-11T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-02-23T13:20:16Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:05Z","tmp":{"short":"CC BY (4.0)","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"},"doi":"10.1103/physrevresearch.2.023154","title":"Induced correlations between impurities in a one-dimensional quenched Bose gas","citation":{"ista":"Mistakidis SI, Volosniev A, Schmelcher P. 2020. Induced correlations between impurities in a one-dimensional quenched Bose gas. Physical Review Research. 2, 023154.","mla":"Mistakidis, S. I., et al. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” <i>Physical Review Research</i>, vol. 2, 023154, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">10.1103/physrevresearch.2.023154</a>.","ama":"Mistakidis SI, Volosniev A, Schmelcher P. Induced correlations between impurities in a one-dimensional quenched Bose gas. <i>Physical Review Research</i>. 2020;2. doi:<a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">10.1103/physrevresearch.2.023154</a>","short":"S.I. Mistakidis, A. Volosniev, P. Schmelcher, Physical Review Research 2 (2020).","apa":"Mistakidis, S. I., Volosniev, A., &#38; Schmelcher, P. (2020). Induced correlations between impurities in a one-dimensional quenched Bose gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">https://doi.org/10.1103/physrevresearch.2.023154</a>","chicago":"Mistakidis, S. I., Artem Volosniev, and P. Schmelcher. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” <i>Physical Review Research</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">https://doi.org/10.1103/physrevresearch.2.023154</a>.","ieee":"S. I. Mistakidis, A. Volosniev, and P. Schmelcher, “Induced correlations between impurities in a one-dimensional quenched Bose gas,” <i>Physical Review Research</i>, vol. 2. American Physical Society, 2020."},"article_number":"023154 "},{"file":[{"date_created":"2020-06-08T06:27:32Z","relation":"main_file","file_name":"2020_ScientificReports_Uroshlev.pdf","access_level":"open_access","file_size":1001724,"date_updated":"2020-07-14T12:48:05Z","checksum":"099e51611a5b7ca04244d03b2faddf33","content_type":"application/pdf","file_id":"7947","creator":"dernst"}],"article_type":"original","author":[{"full_name":"Uroshlev, Leonid A.","first_name":"Leonid A.","last_name":"Uroshlev"},{"full_name":"Abdullaev, Eldar T.","first_name":"Eldar T.","last_name":"Abdullaev"},{"last_name":"Umarova","first_name":"Iren R.","full_name":"Umarova, Iren R."},{"full_name":"Il’Icheva, Irina A.","last_name":"Il’Icheva","first_name":"Irina A."},{"last_name":"Panchenko","first_name":"Larisa A.","full_name":"Panchenko, Larisa A."},{"first_name":"Robert V.","last_name":"Polozov","full_name":"Polozov, Robert V."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Nechipurenko, Yury D.","first_name":"Yury D.","last_name":"Nechipurenko"},{"last_name":"Grokhovsky","first_name":"Sergei L.","full_name":"Grokhovsky, Sergei L."}],"intvolume":"        10","article_processing_charge":"No","_id":"7931","year":"2020","external_id":{"isi":["000560774200007"]},"scopus_import":"1","abstract":[{"text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.","lang":"eng"}],"publication_identifier":{"eissn":["20452322"]},"oa_version":"Published Version","volume":10,"date_created":"2020-06-07T22:00:51Z","type":"journal_article","file_date_updated":"2020-07-14T12:48:05Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-08-21T07:00:17Z","article_number":"8635","citation":{"ieee":"L. A. Uroshlev <i>et al.</i>, “A method for identification of the methylation level of CpG islands from NGS data,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>, vol. 10, 8635, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>.","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>.","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>"},"tmp":{"short":"CC BY (4.0)","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"},"doi":"10.1038/s41598-020-65406-1","title":"A method for identification of the methylation level of CpG islands from NGS data","publication_status":"published","day":"25","isi":1,"publication":"Scientific Reports","ddc":["570"],"oa":1,"month":"05","has_accepted_license":"1","date_published":"2020-05-25T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"FyKo"}]},{"intvolume":"       117","article_processing_charge":"No","_id":"7932","author":[{"id":"3454D55E-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Duo","first_name":"Duo","last_name":"Xu"},{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"first_name":"Xingyu","last_name":"Ma","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0179-9737","full_name":"Ma, Xingyu"},{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","first_name":"Michael","last_name":"Riedl"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"ec_funded":1,"article_type":"original","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"arxiv":1,"oa_version":"Preprint","project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"type":"journal_article","volume":117,"date_created":"2020-06-07T22:00:51Z","external_id":{"isi":["000536797100014"],"arxiv":["2005.11190"]},"year":"2020","scopus_import":"1","page":"11233-11239","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.11190"}],"citation":{"apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., &#38; Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>.","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(21):11233-11239. doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ieee":"D. Xu <i>et al.</i>, “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020."},"title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","doi":"10.1073/pnas.1913716117","quality_controlled":"1","date_updated":"2023-11-30T10:55:13Z","language":[{"iso":"eng"}],"status":"public","date_published":"2020-05-26T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"publication_status":"published","day":"26","issue":"21","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/"}],"record":[{"id":"12726","relation":"dissertation_contains","status":"public"},{"status":"public","id":"14530","relation":"dissertation_contains"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"month":"05","oa":1},{"quality_controlled":"1","date_updated":"2023-08-21T07:05:15Z","language":[{"iso":"eng"}],"article_number":"184104 ","citation":{"apa":"Maslov, M., Lemeshko, M., &#38; Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>.","mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>.","ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104.","ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. 2020;101(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).","ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” <i>Physical Review B</i>, vol. 101, no. 18. American Physical Society, 2020."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.03092"}],"doi":"10.1103/PhysRevB.101.184104","title":"Synthetic spin-orbit coupling mediated by a bosonic environment","day":"01","publication_status":"published","issue":"18","isi":1,"publication":"Physical Review B","oa":1,"month":"05","status":"public","date_published":"2020-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"article_type":"original","author":[{"first_name":"Mikhail","last_name":"Maslov","orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","full_name":"Maslov, Mikhail"},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"}],"ec_funded":1,"intvolume":"       101","article_processing_charge":"No","_id":"7933","year":"2020","external_id":{"arxiv":["1912.03092"],"isi":["000530754700003"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance."}],"publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"arxiv":1,"oa_version":"Preprint","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-06-07T22:00:52Z","volume":101,"type":"journal_article"},{"publication":"IEEE Winter Conference on Applications of Computer Vision","oa":1,"month":"03","day":"01","publication_status":"published","related_material":{"record":[{"id":"8331","relation":"dissertation_contains","status":"deleted"},{"status":"public","id":"8390","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","department":[{"_id":"ChLa"}],"status":"public","date_published":"2020-03-01T00:00:00Z","date_updated":"2023-09-07T13:16:17Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1109/WACV45572.2020.9093288","title":"Localizing grouped instances for efficient detection in low-resource scenarios","article_number":"1716-1725","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.12623"}],"citation":{"ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: <i>IEEE Winter Conference on Applications of Computer Vision</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">10.1109/WACV45572.2020.9093288</a>","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” <i>IEEE Winter Conference on Applications of Computer Vision</i>, 1716–1725, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">10.1109/WACV45572.2020.9093288</a>.","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","apa":"Royer, A., &#38; Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In <i>IEEE Winter Conference on Applications of Computer Vision</i>.  Snowmass Village, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">https://doi.org/10.1109/WACV45572.2020.9093288</a>","chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In <i>IEEE Winter Conference on Applications of Computer Vision</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">https://doi.org/10.1109/WACV45572.2020.9093288</a>.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in <i>IEEE Winter Conference on Applications of Computer Vision</i>,  Snowmass Village, CO, United States, 2020."},"scopus_import":1,"abstract":[{"lang":"eng","text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures."}],"year":"2020","external_id":{"arxiv":["2004.12623"]},"date_created":"2020-06-07T22:00:53Z","type":"conference","conference":{"location":" Snowmass Village, CO, United States","name":"WACV: Winter Conference on Applications of Computer Vision","end_date":"2020-03-05","start_date":"2020-03-01"},"arxiv":1,"publication_identifier":{"isbn":["9781728165530"]},"oa_version":"Preprint","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","first_name":"Amélie","last_name":"Royer"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"article_processing_charge":"No","_id":"7936"},{"publication":"2020 IEEE Winter Conference on Applications of Computer Vision","month":"03","oa":1,"publication_status":"published","day":"01","related_material":{"record":[{"status":"deleted","relation":"dissertation_contains","id":"8331"},{"status":"public","relation":"dissertation_contains","id":"8390"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"IEEE","date_published":"2020-03-01T00:00:00Z","status":"public","date_updated":"2023-09-07T13:16:17Z","language":[{"iso":"eng"}],"quality_controlled":"1","title":"A flexible selection scheme for minimum-effort transfer learning","doi":"10.1109/WACV45572.2020.9093635","main_file_link":[{"url":"http://arxiv.org/abs/2008.11995","open_access":"1"}],"article_number":"2180-2189","citation":{"ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>, Snowmass Village, CO, United States, 2020.","apa":"Royer, A., &#38; Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. Snowmass Village, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">https://doi.org/10.1109/WACV45572.2020.9093635</a>","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">https://doi.org/10.1109/WACV45572.2020.9093635</a>.","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">10.1109/WACV45572.2020.9093635</a>","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>, 2180–2189, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">10.1109/WACV45572.2020.9093635</a>.","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning."}],"external_id":{"arxiv":["2008.11995"]},"year":"2020","type":"conference","date_created":"2020-06-07T22:00:53Z","publication_identifier":{"isbn":["9781728165530"]},"arxiv":1,"conference":{"location":"Snowmass Village, CO, United States","name":"WACV: Winter Conference on Applications of Computer Vision","end_date":"2020-03-05","start_date":"2020-03-01"},"oa_version":"Preprint","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer","first_name":"Amélie"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"article_processing_charge":"No","_id":"7937"},{"date_published":"2020-12-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Gufang Zhao is affiliated to IST Austria, Hausel group until July of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593 of the European Research Council.","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"publication_status":"published","day":"01","publication":"Transformation Groups","isi":1,"month":"12","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.04375","open_access":"1"}],"citation":{"apa":"Yang, Y., &#38; Zhao, G. (2020). The PBW theorem for affine Yangians. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-020-09572-6\">https://doi.org/10.1007/s00031-020-09572-6</a>","chicago":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” <i>Transformation Groups</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00031-020-09572-6\">https://doi.org/10.1007/s00031-020-09572-6</a>.","mla":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” <i>Transformation Groups</i>, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:<a href=\"https://doi.org/10.1007/s00031-020-09572-6\">10.1007/s00031-020-09572-6</a>.","ista":"Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385.","ama":"Yang Y, Zhao G. The PBW theorem for affine Yangians. <i>Transformation Groups</i>. 2020;25:1371-1385. doi:<a href=\"https://doi.org/10.1007/s00031-020-09572-6\">10.1007/s00031-020-09572-6</a>","short":"Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385.","ieee":"Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” <i>Transformation Groups</i>, vol. 25. Springer Nature, pp. 1371–1385, 2020."},"title":"The PBW theorem for affine Yangians","doi":"10.1007/s00031-020-09572-6","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-08-21T07:06:21Z","arxiv":1,"publication_identifier":{"issn":["10834362"],"eissn":["1531586X"]},"oa_version":"Preprint","project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","volume":25,"date_created":"2020-06-07T22:00:55Z","external_id":{"arxiv":["1804.04375"],"isi":["000534874300003"]},"year":"2020","page":"1371-1385","scopus_import":"1","abstract":[{"lang":"eng","text":"We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18]."}],"intvolume":"        25","article_processing_charge":"No","_id":"7940","author":[{"full_name":"Yang, Yaping","id":"360D8648-F248-11E8-B48F-1D18A9856A87","last_name":"Yang","first_name":"Yaping"},{"first_name":"Gufang","last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","full_name":"Zhao, Gufang"}],"ec_funded":1,"article_type":"original"},{"_id":"7942","article_processing_charge":"No","intvolume":"        16","author":[{"full_name":"Hartstein, Máté","last_name":"Hartstein","first_name":"Máté"},{"full_name":"Hsu, Yu Te","first_name":"Yu Te","last_name":"Hsu"},{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic"},{"last_name":"Porras","first_name":"Juan","full_name":"Porras, Juan"},{"full_name":"Loew, Toshinao","last_name":"Loew","first_name":"Toshinao"},{"first_name":"Matthieu Le","last_name":"Tacon","full_name":"Tacon, Matthieu Le"},{"full_name":"Zuo, Huakun","last_name":"Zuo","first_name":"Huakun"},{"last_name":"Wang","first_name":"Jinhua","full_name":"Wang, Jinhua"},{"first_name":"Zengwei","last_name":"Zhu","full_name":"Zhu, Zengwei"},{"first_name":"Mun K.","last_name":"Chan","full_name":"Chan, Mun K."},{"first_name":"Ross D.","last_name":"Mcdonald","full_name":"Mcdonald, Ross D."},{"full_name":"Lonzarich, Gilbert G.","first_name":"Gilbert G.","last_name":"Lonzarich"},{"first_name":"Bernhard","last_name":"Keimer","full_name":"Keimer, Bernhard"},{"full_name":"Sebastian, Suchitra E.","first_name":"Suchitra E.","last_name":"Sebastian"},{"first_name":"Neil","last_name":"Harrison","full_name":"Harrison, Neil"}],"article_type":"letter_note","type":"journal_article","volume":16,"date_created":"2020-06-07T22:00:56Z","arxiv":1,"publication_identifier":{"eissn":["17452481"],"issn":["17452473"]},"oa_version":"Preprint","scopus_import":"1","page":"841-847","abstract":[{"lang":"eng","text":"An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18."}],"external_id":{"isi":["000535464400005"],"arxiv":["2005.14123"]},"year":"2020","title":"Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors","doi":"10.1038/s41567-020-0910-0","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.14123"}],"citation":{"apa":"Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L., … Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-0910-0\">https://doi.org/10.1038/s41567-020-0910-0</a>","chicago":"Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” <i>Nature Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41567-020-0910-0\">https://doi.org/10.1038/s41567-020-0910-0</a>.","ista":"Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J, Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N. 2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 16, 841–847.","mla":"Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” <i>Nature Physics</i>, vol. 16, Springer Nature, 2020, pp. 841–47, doi:<a href=\"https://doi.org/10.1038/s41567-020-0910-0\">10.1038/s41567-020-0910-0</a>.","ama":"Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. <i>Nature Physics</i>. 2020;16:841-847. doi:<a href=\"https://doi.org/10.1038/s41567-020-0910-0\">10.1038/s41567-020-0910-0</a>","short":"M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo, J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian, N. Harrison, Nature Physics 16 (2020) 841–847.","ieee":"M. Hartstein <i>et al.</i>, “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” <i>Nature Physics</i>, vol. 16. Springer Nature, pp. 841–847, 2020."},"language":[{"iso":"eng"}],"date_updated":"2023-08-21T07:06:49Z","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KiMo"}],"publisher":"Springer Nature","acknowledgement":"M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge support from the National Key Research and Development Program of China (grant no. 2016YFA0401704). A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by the National Science Foundation Cooperative Agreement no. DMR-1644779, the state of Florida and the US Department of Energy. Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science of 100 T’ programme.","status":"public","date_published":"2020-08-01T00:00:00Z","publication":"Nature Physics","isi":1,"month":"08","oa":1,"day":"01","publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9708","status":"public"}]}},{"title":"Reconfiguration problems","doi":"10.15479/AT:ISTA:7944","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"alternative_title":["ISTA Thesis"],"citation":{"short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","ama":"Masárová Z. Reconfiguration problems. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7944\">10.15479/AT:ISTA:7944</a>","mla":"Masárová, Zuzana. <i>Reconfiguration Problems</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7944\">10.15479/AT:ISTA:7944</a>.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7944\">https://doi.org/10.15479/AT:ISTA:7944</a>.","apa":"Masárová, Z. (2020). <i>Reconfiguration problems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7944\">https://doi.org/10.15479/AT:ISTA:7944</a>","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020."},"date_updated":"2023-09-07T13:17:37Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:05Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"status":"public","date_published":"2020-06-09T00:00:00Z","has_accepted_license":"1","month":"06","oa":1,"ddc":["516","514"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7950","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5986"}]},"day":"09","publication_status":"published","_id":"7944","article_processing_charge":"No","author":[{"full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana"}],"file":[{"date_updated":"2020-07-14T12:48:05Z","file_size":13661779,"checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945","content_type":"application/pdf","creator":"zmasarov","date_created":"2020-06-08T00:34:00Z","file_name":"THESIS_Zuzka_Masarova.pdf","relation":"main_file","access_level":"open_access"},{"checksum":"45341a35b8f5529c74010b7af43ac188","file_size":32184006,"date_updated":"2020-07-14T12:48:05Z","creator":"zmasarov","file_id":"7946","content_type":"application/zip","relation":"source_file","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","date_created":"2020-06-08T00:35:30Z","access_level":"closed"}],"degree_awarded":"PhD","type":"dissertation","date_created":"2020-06-08T00:49:46Z","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-005-3"]},"abstract":[{"lang":"eng","text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars."}],"page":"160","license":"https://creativecommons.org/licenses/by-sa/4.0/","year":"2020"}]