[{"article_number":"e201907154","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"},{"grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"252C3B08-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","grant_number":"W 1250-B20"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.","ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154.","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154.","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 2020;219(6). doi:10.1083/jcb.201907154","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201907154","ieee":"A. Kopf et al., “Microtubules control cellular shape and coherence in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no. 6. Rockefeller University Press, 2020.","short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020)."},"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","author":[{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Girkontaite","full_name":"Girkontaite, Irute","first_name":"Irute"},{"first_name":"Kerry","full_name":"Tedford, Kerry","last_name":"Tedford"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Thorn-Seshold","full_name":"Thorn-Seshold, Oliver","first_name":"Oliver"},{"id":"E8F27F48-3EBA-11E9-92A1-B709E6697425","first_name":"Dirk","full_name":"Trauner, Dirk","last_name":"Trauner"},{"last_name":"Häcker","full_name":"Häcker, Hans","first_name":"Hans"},{"last_name":"Fischer","full_name":"Fischer, Klaus Dieter","first_name":"Klaus Dieter"},{"first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","last_name":"Kiermaier","orcid":"0000-0001-6165-5738","full_name":"Kiermaier, Eva"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"isi":["000538141100020"],"pmid":["32379884"]},"article_processing_charge":"No","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"day":"01","publication":"The Journal of Cell Biology","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-06-01T00:00:00Z","doi":"10.1083/jcb.201907154","date_created":"2020-05-24T22:00:56Z","_id":"7875","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-21T06:28:17Z","file_date_updated":"2020-11-24T13:25:13Z","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"month":"06","intvolume":" 219","scopus_import":"1","file":[{"file_name":"2020_JCellBiol_Kopf.pdf","date_created":"2020-11-24T13:25:13Z","file_size":7536712,"date_updated":"2020-11-24T13:25:13Z","creator":"dernst","success":1,"file_id":"8801","checksum":"cb0b9c77842ae1214caade7b77e4d82d","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1540-8140"]},"publication_status":"published","issue":"6","volume":219,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1},{"year":"2020","isi":1,"has_accepted_license":"1","publication":"eLife","day":"06","date_created":"2020-05-25T15:01:40Z","doi":"10.7554/elife.55190","date_published":"2020-04-06T00:00:00Z","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","citation":{"chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000531544400001"],"pmid":["32250246"]},"author":[{"last_name":"Schauer","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra"},{"last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","article_number":"e55190","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7890","checksum":"f6aad884cf706846ae9357fcd728f8b5","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-25T15:15:43Z","file_name":"2020_eLife_Schauer.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":7744848}],"ec_funded":1,"volume":9,"related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"04","date_updated":"2023-08-21T06:25:49Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"_id":"7888","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"article_number":"107647","citation":{"ista":"Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.","chicago":"Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647.","short":"I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020).","ieee":"I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell Reports, vol. 31, no. 7. Elsevier, 2020.","ama":"Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 2020;31(7). doi:10.1016/j.celrep.2020.107647","apa":"Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.107647","mla":"Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000535655200005"]},"article_processing_charge":"No","author":[{"last_name":"Parenti","full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria"},{"first_name":"Farah","full_name":"Diab, Farah","last_name":"Diab"},{"full_name":"Gil, Sara Ruiz","last_name":"Gil","first_name":"Sara Ruiz"},{"first_name":"Eskeatnaf","last_name":"Mulugeta","full_name":"Mulugeta, Eskeatnaf"},{"first_name":"Valentina","full_name":"Casa, Valentina","last_name":"Casa"},{"last_name":"Berutti","full_name":"Berutti, Riccardo","first_name":"Riccardo"},{"last_name":"Brouwer","full_name":"Brouwer, Rutger W.W.","first_name":"Rutger W.W."},{"first_name":"Valerie","full_name":"Dupé, Valerie","last_name":"Dupé"},{"first_name":"Juliane","full_name":"Eckhold, Juliane","last_name":"Eckhold"},{"full_name":"Graf, Elisabeth","last_name":"Graf","first_name":"Elisabeth"},{"last_name":"Puisac","full_name":"Puisac, Beatriz","first_name":"Beatriz"},{"last_name":"Ramos","full_name":"Ramos, Feliciano","first_name":"Feliciano"},{"first_name":"Thomas","full_name":"Schwarzmayr, Thomas","last_name":"Schwarzmayr"},{"first_name":"Macarena Moronta","full_name":"Gines, Macarena Moronta","last_name":"Gines"},{"last_name":"Van Staveren","full_name":"Van Staveren, Thomas","first_name":"Thomas"},{"full_name":"Van Ijcken, Wilfred F.J.","last_name":"Van Ijcken","first_name":"Wilfred F.J."},{"last_name":"Strom","full_name":"Strom, Tim M.","first_name":"Tim M."},{"full_name":"Pié, Juan","last_name":"Pié","first_name":"Juan"},{"last_name":"Watrin","full_name":"Watrin, Erwan","first_name":"Erwan"},{"first_name":"Frank J.","last_name":"Kaiser","full_name":"Kaiser, Frank J."},{"last_name":"Wendt","full_name":"Wendt, Kerstin S.","first_name":"Kerstin S."}],"title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","oa":1,"publisher":"Elsevier","quality_controlled":"1","year":"2020","has_accepted_license":"1","isi":1,"publication":"Cell Reports","day":"19","date_created":"2020-05-24T22:00:57Z","date_published":"2020-05-19T00:00:00Z","doi":"10.1016/j.celrep.2020.107647","_id":"7877","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-21T06:27:47Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"GaNo"}],"abstract":[{"lang":"eng","text":"The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 31","month":"05","publication_status":"published","publication_identifier":{"eissn":["22111247"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7892","checksum":"64d8f7467731ee5c166b10b939b8310b","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-05-26T11:05:01Z","file_name":"2020_CellReports_Parenti.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":4695682}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":31,"issue":"7"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7878","file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-08-21T06:26:50Z","intvolume":" 9","month":"05","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":9,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":4832050,"date_created":"2020-05-26T09:34:54Z","file_name":"2020_eLife_Bao.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8ea99bb6660cc407dbdb00c173b01683","file_id":"7891"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"article_number":"e56839","title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","article_processing_charge":"No","external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"author":[{"last_name":"Bao","full_name":"Bao, Jin","first_name":"Jin"},{"first_name":"Michael","full_name":"Graupner, Michael","last_name":"Graupner"},{"first_name":"Guadalupe","last_name":"Astorga","full_name":"Astorga, Guadalupe"},{"first_name":"Thibault","last_name":"Collin","full_name":"Collin, Thibault"},{"last_name":"Jalil","full_name":"Jalil, Abdelali","first_name":"Abdelali"},{"full_name":"Indriati, Dwi Wahyu","last_name":"Indriati","first_name":"Dwi Wahyu"},{"full_name":"Bradley, Jonathan","last_name":"Bradley","first_name":"Jonathan"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Llano","full_name":"Llano, Isabel","first_name":"Isabel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56839","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. eLife. 2020;9. doi:10.7554/eLife.56839","short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","ieee":"J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol. 9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839.","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.","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.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56839."},"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","date_created":"2020-05-24T22:00:58Z","date_published":"2020-05-13T00:00:00Z","doi":"10.7554/eLife.56839","publication":"eLife","day":"13","year":"2020","isi":1,"has_accepted_license":"1"},{"oa":1,"publisher":"ASBMB Publications","quality_controlled":"1","page":"5229-5244","date_created":"2020-05-24T22:00:59Z","date_published":"2020-04-17T00:00:00Z","doi":"10.1074/jbc.RA120.012628","year":"2020","isi":1,"publication":"Journal of Biological Chemistry","day":"17","external_id":{"isi":["000530288000006"],"pmid":["32132171"]},"article_processing_charge":"No","author":[{"full_name":"Fagan, Rita R.","last_name":"Fagan","first_name":"Rita R."},{"first_name":"Patrick J.","full_name":"Kearney, Patrick J.","last_name":"Kearney"},{"full_name":"Sweeney, Carolyn G.","last_name":"Sweeney","first_name":"Carolyn G."},{"first_name":"Dino","last_name":"Luethi","full_name":"Luethi, Dino"},{"last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Klaus","last_name":"Schicker","full_name":"Schicker, Klaus"},{"first_name":"Brian S.","full_name":"Alejandro, Brian S.","last_name":"Alejandro"},{"first_name":"Lauren C.","last_name":"O'Connor","full_name":"O'Connor, Lauren C."},{"last_name":"Sitte","full_name":"Sitte, Harald H.","first_name":"Harald H."},{"first_name":"Haley E.","full_name":"Melikian, Haley E.","last_name":"Melikian"}],"title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","citation":{"mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628.","ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628","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. Journal of Biological Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628","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.","ieee":"R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” Journal of Biological Chemistry, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","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.” Journal of Biological Chemistry. ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://escholarship.umassmed.edu/oapubs/4187","open_access":"1"}],"scopus_import":"1","intvolume":" 295","month":"04","abstract":[{"lang":"eng","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. "}],"oa_version":"Submitted Version","pmid":1,"volume":295,"issue":"16","publication_status":"published","publication_identifier":{"eissn":["1083351X"],"issn":["00219258"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"7880","department":[{"_id":"SaSi"}],"date_updated":"2023-08-21T06:26:22Z"},{"page":"721-723","doi":"10.1016/j.immuni.2020.04.020","date_published":"2020-05-19T00:00:00Z","date_created":"2020-05-24T22:00:57Z","isi":1,"year":"2020","day":"19","publication":"Immunity","publisher":"Elsevier","quality_controlled":"1","oa":1,"author":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"}],"external_id":{"isi":["000535371100002"]},"article_processing_charge":"No","title":"T cells: Bridge-and-channel commute to the white pulp","citation":{"mla":"Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:10.1016/j.immuni.2020.04.020.","apa":"Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020","ama":"Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020","short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","ieee":"M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.","chicago":"Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.","ista":"Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"5","volume":52,"publication_identifier":{"eissn":["10974180"],"issn":["10747613"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf"}],"month":"05","intvolume":" 52","abstract":[{"lang":"eng","text":"In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. "}],"oa_version":"Published Version","department":[{"_id":"MiSi"}],"date_updated":"2023-08-21T06:27:18Z","type":"journal_article","article_type":"original","status":"public","_id":"7876"},{"article_number":"e55351","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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).","ieee":"J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” eLife, vol. 9. eLife Sciences Publications, 2020.","ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 2020;9. doi:10.7554/eLife.55351","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. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.55351","mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9, e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351.","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.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351."},"title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","author":[{"full_name":"Damiano-Guercio, Julia","last_name":"Damiano-Guercio","first_name":"Julia"},{"first_name":"Laëtitia","full_name":"Kurzawa, Laëtitia","last_name":"Kurzawa"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","full_name":"Müller, Jan","last_name":"Müller"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161"},{"first_name":"Matthias","full_name":"Schaks, Matthias","last_name":"Schaks"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Nemethova, Maria","last_name":"Nemethova"},{"first_name":"Thomas","full_name":"Pokrant, Thomas","last_name":"Pokrant"},{"full_name":"Brühmann, Stefan","last_name":"Brühmann","first_name":"Stefan"},{"full_name":"Linkner, Joern","last_name":"Linkner","first_name":"Joern"},{"full_name":"Blanchoin, Laurent","last_name":"Blanchoin","first_name":"Laurent"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"},{"first_name":"Klemens","full_name":"Rottner, Klemens","last_name":"Rottner"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"}],"article_processing_charge":"No","external_id":{"isi":["000537208000001"]},"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"day":"11","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.7554/eLife.55351","date_published":"2020-05-11T00:00:00Z","date_created":"2020-05-31T22:00:49Z","_id":"7909","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-21T06:32:25Z","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:48:05Z","oa_version":"Published Version","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"}],"month":"05","intvolume":" 9","scopus_import":"1","file":[{"file_id":"7914","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-06-02T10:35:37Z","file_name":"2020_eLife_Damiano_Guercio.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:05Z","file_size":10535713}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","volume":9,"ec_funded":1},{"author":[{"last_name":"Wang","full_name":"Wang, Han Ying","first_name":"Han Ying"},{"first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"last_name":"Yamashita","full_name":"Yamashita, Takayuki","first_name":"Takayuki"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"external_id":{"isi":["000535694700004"]},"article_processing_charge":"No","title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","citation":{"ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020","short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020.","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020.","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.","chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"4103-4115","date_published":"2020-05-20T00:00:00Z","doi":"10.1523/JNEUROSCI.2946-19.2020","date_created":"2020-05-31T22:00:48Z","has_accepted_license":"1","isi":1,"year":"2020","day":"20","publication":"Journal of Neuroscience","publisher":"Society for Neuroscience","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"RySh"}],"date_updated":"2023-08-21T06:31:25Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7908","volume":40,"issue":"21","publication_identifier":{"eissn":["15292401"]},"publication_status":"published","file":[{"file_name":"2020_JourNeuroscience_Wang.pdf","date_created":"2020-06-02T09:12:16Z","creator":"dernst","file_size":3817360,"date_updated":"2020-07-14T12:48:05Z","file_id":"7912","checksum":"6571607ea9036154b67cc78e848a7f7d","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 40","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:48:05Z","date_updated":"2023-08-21T07:00:17Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7931","volume":10,"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7947","checksum":"099e51611a5b7ca04244d03b2faddf33","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_ScientificReports_Uroshlev.pdf","date_created":"2020-06-08T06:27:32Z","creator":"dernst","file_size":1001724,"date_updated":"2020-07-14T12:48:05Z"}],"scopus_import":"1","intvolume":" 10","month":"05","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"}],"oa_version":"Published Version","external_id":{"isi":["000560774200007"]},"article_processing_charge":"No","author":[{"first_name":"Leonid A.","full_name":"Uroshlev, Leonid A.","last_name":"Uroshlev"},{"full_name":"Abdullaev, Eldar T.","last_name":"Abdullaev","first_name":"Eldar T."},{"first_name":"Iren R.","full_name":"Umarova, Iren R.","last_name":"Umarova"},{"first_name":"Irina A.","last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A."},{"first_name":"Larisa A.","last_name":"Panchenko","full_name":"Panchenko, Larisa A."},{"last_name":"Polozov","full_name":"Polozov, Robert V.","first_name":"Robert V."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Yury D.","last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D."},{"last_name":"Grokhovsky","full_name":"Grokhovsky, Sergei L.","first_name":"Sergei L."}],"title":"A method for identification of the methylation level of CpG islands from NGS data","citation":{"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.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1.","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.","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.","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).","ieee":"L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1","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. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"8635","date_created":"2020-06-07T22:00:51Z","date_published":"2020-05-25T00:00:00Z","doi":"10.1038/s41598-020-65406-1","year":"2020","isi":1,"has_accepted_license":"1","publication":"Scientific Reports","day":"25","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"_id":"7933","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-21T07:05:15Z","department":[{"_id":"MiLe"}],"oa_version":"Preprint","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."}],"intvolume":" 101","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1912.03092","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"ec_funded":1,"volume":101,"issue":"18","article_number":"184104 ","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104.","ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” Physical Review B, vol. 101, no. 18. American Physical Society, 2020.","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).","apa":"Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.184104","ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104","mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:10.1103/PhysRevB.101.184104."},"title":"Synthetic spin-orbit coupling mediated by a bosonic environment","external_id":{"isi":["000530754700003"],"arxiv":["1912.03092"]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail","last_name":"Maslov","first_name":"Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review B","day":"01","year":"2020","isi":1,"date_created":"2020-06-07T22:00:52Z","doi":"10.1103/PhysRevB.101.184104","date_published":"2020-05-01T00:00:00Z"},{"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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Physics","day":"01","year":"2020","isi":1,"date_created":"2020-06-07T22:00:56Z","doi":"10.1038/s41567-020-0910-0","date_published":"2020-08-01T00:00:00Z","page":"841-847","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0910-0.","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.” Nature Physics, vol. 16, Springer Nature, 2020, pp. 841–47, doi:10.1038/s41567-020-0910-0.","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. Nature Physics. 2020;16:841-847. doi:10.1038/s41567-020-0910-0","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. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0910-0","ieee":"M. Hartstein et al., “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” Nature Physics, vol. 16. Springer Nature, pp. 841–847, 2020.","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."},"title":"Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors","external_id":{"arxiv":["2005.14123"],"isi":["000535464400005"]},"article_processing_charge":"No","author":[{"first_name":"Máté","last_name":"Hartstein","full_name":"Hartstein, Máté"},{"first_name":"Yu Te","full_name":"Hsu, Yu Te","last_name":"Hsu"},{"last_name":"Modic","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A"},{"last_name":"Porras","full_name":"Porras, Juan","first_name":"Juan"},{"last_name":"Loew","full_name":"Loew, Toshinao","first_name":"Toshinao"},{"full_name":"Tacon, Matthieu Le","last_name":"Tacon","first_name":"Matthieu Le"},{"first_name":"Huakun","full_name":"Zuo, Huakun","last_name":"Zuo"},{"full_name":"Wang, Jinhua","last_name":"Wang","first_name":"Jinhua"},{"first_name":"Zengwei","full_name":"Zhu, Zengwei","last_name":"Zhu"},{"first_name":"Mun K.","last_name":"Chan","full_name":"Chan, Mun K."},{"last_name":"Mcdonald","full_name":"Mcdonald, Ross D.","first_name":"Ross D."},{"first_name":"Gilbert G.","full_name":"Lonzarich, Gilbert G.","last_name":"Lonzarich"},{"first_name":"Bernhard","last_name":"Keimer","full_name":"Keimer, Bernhard"},{"first_name":"Suchitra E.","full_name":"Sebastian, Suchitra E.","last_name":"Sebastian"},{"first_name":"Neil","full_name":"Harrison, Neil","last_name":"Harrison"}],"oa_version":"Preprint","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."}],"intvolume":" 16","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/2005.14123","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["17452473"],"eissn":["17452481"]},"volume":16,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9708"}]},"_id":"7942","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-08-21T07:06:49Z","department":[{"_id":"KiMo"}]},{"type":"journal_article","article_type":"original","status":"public","_id":"7948","department":[{"_id":"EvBe"}],"date_updated":"2023-08-21T07:07:30Z","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-02619371"}],"month":"07","intvolume":" 71","abstract":[{"lang":"eng","text":"In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture."}],"oa_version":"Submitted Version","pmid":1,"volume":71,"issue":"15","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Maghiaoui","full_name":"Maghiaoui, A","first_name":"A"},{"first_name":"E","full_name":"Bouguyon, E","last_name":"Bouguyon"},{"last_name":"Cuesta","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"first_name":"F","last_name":"Perrine-Walker","full_name":"Perrine-Walker, F"},{"full_name":"Alcon, C","last_name":"Alcon","first_name":"C"},{"last_name":"Krouk","full_name":"Krouk, G","first_name":"G"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Nacry, P","last_name":"Nacry","first_name":"P"},{"full_name":"Gojon, A","last_name":"Gojon","first_name":"A"},{"first_name":"L","full_name":"Bach, L","last_name":"Bach"}],"external_id":{"pmid":["32428238"],"isi":["000553127600013"]},"article_processing_charge":"No","title":"The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate","citation":{"ista":"Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A, Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 71(15), 4480–4494.","chicago":"Maghiaoui, A, E Bouguyon, Candela Cuesta, F Perrine-Walker, C Alcon, G Krouk, Eva Benková, P Nacry, A Gojon, and L Bach. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa242.","ama":"Maghiaoui A, Bouguyon E, Cuesta C, et al. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 2020;71(15):4480-4494. doi:10.1093/jxb/eraa242","apa":"Maghiaoui, A., Bouguyon, E., Cuesta, C., Perrine-Walker, F., Alcon, C., Krouk, G., … Bach, L. (2020). The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa242","short":"A. Maghiaoui, E. Bouguyon, C. Cuesta, F. Perrine-Walker, C. Alcon, G. Krouk, E. Benková, P. Nacry, A. Gojon, L. Bach, Journal of Experimental Botany 71 (2020) 4480–4494.","ieee":"A. Maghiaoui et al., “The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate,” Journal of Experimental Botany, vol. 71, no. 15. Oxford University Press, pp. 4480–4494, 2020.","mla":"Maghiaoui, A., et al. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany, vol. 71, no. 15, Oxford University Press, 2020, pp. 4480–94, doi:10.1093/jxb/eraa242."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"page":"4480-4494","date_published":"2020-07-25T00:00:00Z","doi":"10.1093/jxb/eraa242","date_created":"2020-06-08T10:10:28Z","isi":1,"year":"2020","day":"25","publication":"Journal of Experimental Botany"},{"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000534874300003"],"arxiv":["1804.04375"]},"article_processing_charge":"No","author":[{"full_name":"Yang, Yaping","last_name":"Yang","first_name":"Yaping","id":"360D8648-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhao, Gufang","last_name":"Zhao","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"}],"title":"The PBW theorem for affine Yangians","citation":{"apa":"Yang, Y., & Zhao, G. (2020). The PBW theorem for affine Yangians. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-020-09572-6","ama":"Yang Y, Zhao G. The PBW theorem for affine Yangians. Transformation Groups. 2020;25:1371-1385. doi:10.1007/s00031-020-09572-6","ieee":"Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” Transformation Groups, vol. 25. Springer Nature, pp. 1371–1385, 2020.","short":"Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385.","mla":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:10.1007/s00031-020-09572-6.","ista":"Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385.","chicago":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups. Springer Nature, 2020. https://doi.org/10.1007/s00031-020-09572-6."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","page":"1371-1385","date_created":"2020-06-07T22:00:55Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s00031-020-09572-6","year":"2020","isi":1,"publication":"Transformation Groups","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"7940","department":[{"_id":"TaHa"}],"date_updated":"2023-08-21T07:06:21Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04375"}],"scopus_import":"1","intvolume":" 25","month":"12","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]."}],"oa_version":"Preprint","ec_funded":1,"volume":25,"publication_status":"published","publication_identifier":{"eissn":["1531586X"],"issn":["10834362"]},"language":[{"iso":"eng"}]},{"title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","department":[{"_id":"KiMo"}],"article_processing_charge":"No","author":[{"first_name":"Mate","last_name":"Hartstein","full_name":"Hartstein, Mate"},{"full_name":"Hsu, Yu-Te","last_name":"Hsu","first_name":"Yu-Te"},{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","last_name":"Modic"},{"first_name":"Juan","full_name":"Porras, Juan","last_name":"Porras"},{"full_name":"Loew, Toshinao","last_name":"Loew","first_name":"Toshinao"},{"last_name":"Le Tacon","full_name":"Le Tacon, Matthieu","first_name":"Matthieu"},{"last_name":"Zuo","full_name":"Zuo, Huakun","first_name":"Huakun"},{"full_name":"Wang, Jinhua","last_name":"Wang","first_name":"Jinhua"},{"first_name":"Zengwei","full_name":"Zhu, Zengwei","last_name":"Zhu"},{"full_name":"Chan, Mun","last_name":"Chan","first_name":"Mun"},{"full_name":"McDonald, Ross","last_name":"McDonald","first_name":"Ross"},{"last_name":"Lonzarich","full_name":"Lonzarich, Gilbert","first_name":"Gilbert"},{"full_name":"Keimer, Bernhard","last_name":"Keimer","first_name":"Bernhard"},{"full_name":"Sebastian, Suchitra","last_name":"Sebastian","first_name":"Suchitra"},{"full_name":"Harrison, Neil","last_name":"Harrison","first_name":"Neil"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-21T07:06:48Z","citation":{"ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169.","chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169","apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169","short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020).","ieee":"M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","mla":"Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"9708","date_created":"2021-07-23T10:00:35Z","related_material":{"record":[{"relation":"used_in_publication","id":"7942","status":"public"}]},"doi":"10.17863/cam.50169","date_published":"2020-05-29T00:00:00Z","day":"29","year":"2020","has_accepted_license":"1","month":"05","oa":1,"main_file_link":[{"url":"https://doi.org/10.17863/CAM.50169","open_access":"1"}],"publisher":"Apollo - University of Cambridge","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided."}]},{"acknowledgement":"Pranav Ashok, Jan Křetínský and Maximilian Weininger were funded in part by TUM IGSSE Grant 10.06 (PARSEC) and the German Research Foundation (DFG) project KR 4890/2-1\r\n“Statistical Unbounded Verification”. Krishnendu Chatterjee was supported by the ERC CoG 863818 (ForM-SMArt) and Vienna Science and Technology Fund (WWTF) Project ICT15-\r\n003. Tobias Winkler was supported by the RTG 2236 UnRAVe.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","publication":"Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science ","day":"08","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-06-14T22:00:48Z","doi":"10.1145/3373718.3394761","date_published":"2020-07-08T00:00:00Z","page":"102-115","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Ashok, Pranav, et al. “Approximating Values of Generalized-Reachability Stochastic Games.” Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–15, doi:10.1145/3373718.3394761.","apa":"Ashok, P., Chatterjee, K., Kretinsky, J., Weininger, M., & Winkler, T. (2020). Approximating values of generalized-reachability stochastic games. In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 102–115). Saarbrücken, Germany: Association for Computing Machinery. https://doi.org/10.1145/3373718.3394761","ama":"Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. Approximating values of generalized-reachability stochastic games. In: Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . Association for Computing Machinery; 2020:102-115. doi:10.1145/3373718.3394761","ieee":"P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, and T. Winkler, “Approximating values of generalized-reachability stochastic games,” in Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Saarbrücken, Germany, 2020, pp. 102–115.","short":"P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, T. Winkler, in:, Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–115.","chicago":"Ashok, Pranav, Krishnendu Chatterjee, Jan Kretinsky, Maximilian Weininger, and Tobias Winkler. “Approximating Values of Generalized-Reachability Stochastic Games.” In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , 102–15. Association for Computing Machinery, 2020. https://doi.org/10.1145/3373718.3394761.","ista":"Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. 2020. Approximating values of generalized-reachability stochastic games. Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . LICS: Symposium on Logic in Computer Science, 102–115."},"title":"Approximating values of generalized-reachability stochastic games","external_id":{"isi":["000665014900010"],"arxiv":["1908.05106"]},"article_processing_charge":"No","author":[{"last_name":"Ashok","full_name":"Ashok, Pranav","first_name":"Pranav"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan"},{"first_name":"Maximilian","full_name":"Weininger, Maximilian","last_name":"Weininger"},{"full_name":"Winkler, Tobias","last_name":"Winkler","first_name":"Tobias"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound."}],"month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d0d0288fe991dd16cf5f02598b794240","file_id":"8804","success":1,"creator":"dernst","date_updated":"2020-11-25T09:38:14Z","file_size":1001395,"date_created":"2020-11-25T09:38:14Z","file_name":"2020_LICS_Ashok.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9781450371049"]},"ec_funded":1,"_id":"7955","status":"public","conference":{"end_date":"2020-07-11","location":"Saarbrücken, Germany","start_date":"2020-07-08","name":"LICS: Symposium on Logic in Computer Science"},"type":"conference","ddc":["000"],"date_updated":"2023-08-21T08:24:36Z","file_date_updated":"2020-11-25T09:38:14Z","department":[{"_id":"KrCh"}]},{"project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"}],"title":"Neurodevelopmental disorders: From genetics to functional pathways","author":[{"full_name":"Parenti, Ilaria","last_name":"Parenti","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria"},{"first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"full_name":"Schön, Hanna","last_name":"Schön","first_name":"Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"external_id":{"pmid":["32507511"],"isi":["000553090600008"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.","chicago":"Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.","ieee":"I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” Trends in Neurosciences, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.","short":"I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621.","ama":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621. doi:10.1016/j.tins.2020.05.004","apa":"Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004","mla":"Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:10.1016/j.tins.2020.05.004."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N.","date_published":"2020-08-01T00:00:00Z","doi":"10.1016/j.tins.2020.05.004","date_created":"2020-06-14T22:00:49Z","page":"608-621","day":"01","publication":"Trends in Neurosciences","has_accepted_license":"1","isi":1,"year":"2020","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7957","file_date_updated":"2020-11-25T09:43:40Z","department":[{"_id":"GaNo"}],"ddc":["570"],"date_updated":"2023-08-21T08:25:31Z","month":"08","intvolume":" 43","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.","lang":"eng"}],"issue":"8","volume":43,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8805","checksum":"67db0251b1d415ae59005f876fcf9e34","file_size":1439550,"date_updated":"2020-11-25T09:43:40Z","creator":"dernst","file_name":"2020_TrendsNeuroscience_Parenti.pdf","date_created":"2020-11-25T09:43:40Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01662236"],"eissn":["1878108X"]},"publication_status":"published"},{"date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s00454-020-00205-z","date_created":"2020-06-14T22:00:50Z","page":"304-323","day":"01","publication":"Discrete and Computational Geometry","isi":1,"year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We are very grateful to Pavel Paták for many helpful discussions and remarks. We also thank the referees for helpful comments, which greatly improved the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK was also partially supported by NSF grant DMS1300120. The research stay of ZP at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF.","title":"Intersection patterns of planar sets","author":[{"full_name":"Kalai, Gil","last_name":"Kalai","first_name":"Gil"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana"}],"external_id":{"arxiv":["1907.00885"],"isi":["000537329400001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z.","ama":"Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z","apa":"Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z","ieee":"G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020.","short":"G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323.","chicago":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z.","ista":"Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete and Computational Geometry. 64, 304–323."},"volume":64,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"publication_status":"published","month":"09","intvolume":" 64","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.00885"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces."}],"department":[{"_id":"UlWa"}],"date_updated":"2023-08-21T08:26:34Z","status":"public","type":"journal_article","article_type":"original","_id":"7960"},{"month":"06","intvolume":" 63","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.06710"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets."}],"volume":63,"issue":"4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"7962","department":[{"_id":"HeEd"}],"date_updated":"2023-08-21T08:49:18Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"doi":"10.1007/s00454-020-00213-z","date_published":"2020-06-05T00:00:00Z","date_created":"2020-06-14T22:00:51Z","page":"888-917","day":"05","publication":"Discrete and Computational Geometry","isi":1,"year":"2020","project":[{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"title":"Almost all string graphs are intersection graphs of plane convex sets","author":[{"first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János","last_name":"Pach"},{"first_name":"Bruce","full_name":"Reed, Bruce","last_name":"Reed"},{"full_name":"Yuditsky, Yelena","last_name":"Yuditsky","first_name":"Yelena"}],"article_processing_charge":"No","external_id":{"arxiv":["1803.06710"],"isi":["000538229000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z.","short":"J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020) 888–917.","ieee":"J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection graphs of plane convex sets,” Discrete and Computational Geometry, vol. 63, no. 4. Springer Nature, pp. 888–917, 2020.","apa":"Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00213-z","ama":"Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917. doi:10.1007/s00454-020-00213-z","chicago":"Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z.","ista":"Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917."}},{"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_size":1475657,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_name":"2020_NatureComm_Bayesian.pdf","date_created":"2020-06-22T11:24:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4c96babd4cfb0d153334f6c598c0bacb","file_id":"8000"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19099-9"}]},"volume":11,"abstract":[{"lang":"eng","text":"Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. "}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 11","month":"06","date_updated":"2023-08-22T07:13:09Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"MaRo"}],"_id":"7999","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"08","date_created":"2020-06-22T11:18:25Z","date_published":"2020-06-08T00:00:00Z","doi":"10.1038/s41467-020-16520-1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"chicago":"Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen, R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1.","ista":"Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 11, 2865.","mla":"Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature, 2020, doi:10.1038/s41467-020-16520-1.","ama":"Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1","apa":"Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen, C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1","ieee":"D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020.","short":"D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen, R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae, N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J. Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000541702400004"],"pmid":["32513961"]},"author":[{"first_name":"D","full_name":"Trejo Banos, D","last_name":"Trejo Banos"},{"full_name":"McCartney, DL","last_name":"McCartney","first_name":"DL"},{"full_name":"Patxot, M","last_name":"Patxot","first_name":"M"},{"first_name":"L","last_name":"Anchieri","full_name":"Anchieri, L"},{"full_name":"Battram, T","last_name":"Battram","first_name":"T"},{"first_name":"C","full_name":"Christiansen, C","last_name":"Christiansen"},{"first_name":"R","full_name":"Costeira, R","last_name":"Costeira"},{"full_name":"Walker, RM","last_name":"Walker","first_name":"RM"},{"last_name":"Morris","full_name":"Morris, SW","first_name":"SW"},{"last_name":"Campbell","full_name":"Campbell, A","first_name":"A"},{"first_name":"Q","full_name":"Zhang, Q","last_name":"Zhang"},{"first_name":"DJ","full_name":"Porteous, DJ","last_name":"Porteous"},{"full_name":"McRae, AF","last_name":"McRae","first_name":"AF"},{"last_name":"Wray","full_name":"Wray, NR","first_name":"NR"},{"first_name":"PM","last_name":"Visscher","full_name":"Visscher, PM"},{"first_name":"CS","full_name":"Haley, CS","last_name":"Haley"},{"first_name":"KL","full_name":"Evans, KL","last_name":"Evans"},{"last_name":"Deary","full_name":"Deary, IJ","first_name":"IJ"},{"last_name":"McIntosh","full_name":"McIntosh, AM","first_name":"AM"},{"first_name":"G","last_name":"Hemani","full_name":"Hemani, G"},{"last_name":"Bell","full_name":"Bell, JT","first_name":"JT"},{"first_name":"RE","last_name":"Marioni","full_name":"Marioni, RE"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}],"title":"Bayesian reassessment of the epigenetic architecture of complex traits","article_number":"2865"},{"file":[{"file_name":"2020_Evolution_Perini.pdf","date_created":"2020-11-25T10:49:48Z","creator":"dernst","file_size":1080810,"date_updated":"2020-11-25T10:49:48Z","success":1,"checksum":"56235bf1e2a9e25f96196bb13b6b754d","file_id":"8808","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15585646"],"issn":["00143820"]},"publication_status":"published","volume":74,"related_material":{"record":[{"id":"8809","status":"public","relation":"research_data"}]},"issue":"7","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"month":"07","intvolume":" 74","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-22T07:13:38Z","file_date_updated":"2020-11-25T10:49:48Z","department":[{"_id":"NiBa"}],"_id":"7995","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication":"Evolution","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1111/evo.14027","date_published":"2020-07-01T00:00:00Z","date_created":"2020-06-22T09:14:21Z","page":"1482-1497","acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","quality_controlled":"1","publisher":"Wiley","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027.","ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027.","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497."},"title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","author":[{"first_name":"Samuel","full_name":"Perini, Samuel","last_name":"Perini"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"article_processing_charge":"No","external_id":{"isi":["000539780800001"]},"project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}]},{"publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"month":"07","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"oa_version":"Published Version","date_published":"2020-07-01T00:00:00Z","doi":"10.5061/dryad.qrfj6q5cn","related_material":{"record":[{"relation":"used_in_publication","id":"7995","status":"public"}]},"date_created":"2020-11-25T11:07:25Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","has_accepted_license":"1","year":"2020","day":"01","type":"research_data_reference","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","_id":"8809","author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Rafajlovic, Marina","last_name":"Rafajlovic","first_name":"Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"article_processing_charge":"No","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T07:13:37Z","citation":{"ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739"}],"article_processing_charge":"No","external_id":{"isi":["000556135600004"],"pmid":["32492366"]},"author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","full_name":"Zhang, Xiaomin","last_name":"Zhang"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"title":"Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation","citation":{"ama":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013","apa":"Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.013","short":"D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020) 509–521.","ieee":"D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3. Elsevier, pp. 509–521, 2020.","mla":"Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21, doi:10.1016/j.neuron.2020.05.013.","ista":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 107(3), 509–521.","chicago":"Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung ( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs. Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian Marr for excellent technical assistance and cell reconstruction; Christina Altmutter for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of IST Austria for support.","page":"509-521","date_created":"2020-06-22T13:29:05Z","date_published":"2020-08-05T00:00:00Z","doi":"10.1016/j.neuron.2020.05.013","year":"2020","has_accepted_license":"1","isi":1,"publication":"Neuron","day":"05","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","_id":"8001","file_date_updated":"2020-11-25T11:23:02Z","department":[{"_id":"PeJo"}],"date_updated":"2023-08-22T07:45:25Z","ddc":["570"],"scopus_import":"1","intvolume":" 107","month":"08","abstract":[{"lang":"eng","text":"Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"volume":107,"issue":"3","related_material":{"link":[{"url":"https://ist.ac.at/en/news/possible-physical-trace-of-short-term-memory-found/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","publication_identifier":{"issn":["0896-6273"],"eissn":["10974199"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4390833,"date_updated":"2020-11-25T11:23:02Z","file_name":"2020_Neuron_Vandael.pdf","date_created":"2020-11-25T11:23:02Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"4030b2be0c9625d54694a1e9fb00305e","file_id":"8811"}]},{"oa":1,"publisher":"IOP Publishing","quality_controlled":"1","year":"2020","has_accepted_license":"1","isi":1,"publication":"Quantum Science and Technology","day":"25","date_created":"2020-06-29T07:59:35Z","doi":"10.1088/2058-9565/ab8dce","date_published":"2020-05-25T00:00:00Z","article_number":"034011","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Integrating superconducting quantum circuits","grant_number":"F07105","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020). Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab8dce","ama":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce","short":"J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and Technology 5 (2020).","ieee":"J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing, 2020.","mla":"Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce.","ista":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 5(3), 034011.","chicago":"Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab8dce."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000539300800001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"first_name":"M.","full_name":"Kalaee, M.","last_name":"Kalaee"},{"last_name":"Norte","full_name":"Norte, R.","first_name":"R."},{"first_name":"A.","full_name":"Pitanti, A.","last_name":"Pitanti"},{"first_name":"O.","full_name":"Painter, O.","last_name":"Painter"}],"title":"Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator","abstract":[{"text":"Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 5","month":"05","publication_status":"published","publication_identifier":{"eissn":["20589565"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8072","checksum":"8f25f05053f511f892ae8fa93f341e61","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_QuantumSciTechnol_Fink.pdf","date_created":"2020-06-30T10:29:10Z","file_size":2600967,"date_updated":"2020-07-14T12:48:08Z","creator":"cziletti"}],"ec_funded":1,"issue":"3","volume":5,"_id":"8038","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T07:49:01Z","ddc":["530"],"department":[{"_id":"JoFi"}],"file_date_updated":"2020-07-14T12:48:08Z"},{"ddc":["530"],"date_updated":"2023-08-22T07:47:30Z","department":[{"_id":"ScWa"}],"file_date_updated":"2020-07-14T12:48:08Z","_id":"8036","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"cziletti","date_updated":"2020-07-14T12:48:08Z","file_size":1907821,"date_created":"2020-06-29T13:21:24Z","file_name":"2020_CommunicationsPhysics_Collard.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"ed984f7a393f19140b5279a54a3336ad","file_id":"8045"}],"publication_status":"published","publication_identifier":{"eissn":["23993650"]},"ec_funded":1,"volume":3,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves."}],"intvolume":" 3","month":"06","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature, 2020, doi:10.1038/s42005-020-0380-9.","ieee":"Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal waves induce locomotion in self-assemblies,” Communications Physics, vol. 3. Springer Nature, 2020.","short":"Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020).","ama":"Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9","apa":"Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-0380-9","chicago":"Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9.","ista":"Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 3, 112."},"title":"Magnetically powered metachronal waves induce locomotion in self-assemblies","external_id":{"isi":["000543328000002"]},"article_processing_charge":"No","author":[{"full_name":"Collard, Ylona","last_name":"Collard","first_name":"Ylona"},{"first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean"},{"full_name":"Vandewalle, Nicolas","last_name":"Vandewalle","first_name":"Nicolas"}],"article_number":"112","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"Communications Physics","day":"19","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-06-29T07:59:35Z","date_published":"2020-06-19T00:00:00Z","doi":"10.1038/s42005-020-0380-9","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"acknowledgement":"The authors thank S. Zammert and B. Budanur for useful discussions. J. F. Gibson is gratefully acknowledged for the development and the maintenance of the code Channelflow. Y.D. would like to thank P. Schlatter and D. S. Henningson for an early collaboration on a similar topic in the case of plane Couette flow during the years 2008–2013.","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"day":"25","publication":"Journal of Fluid Mechanics","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1017/jfm.2020.322","date_published":"2020-08-25T00:00:00Z","date_created":"2020-06-29T07:59:35Z","article_number":"A7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Paranjape CS, Duguet Y, Hof B. 2020. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 897, A7.","chicago":"Paranjape, Chaitanya S, Yohann Duguet, and Björn Hof. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2020. https://doi.org/10.1017/jfm.2020.322.","short":"C.S. Paranjape, Y. Duguet, B. Hof, Journal of Fluid Mechanics 897 (2020).","ieee":"C. S. Paranjape, Y. Duguet, and B. Hof, “Oblique stripe solutions of channel flow,” Journal of Fluid Mechanics, vol. 897. Cambridge University Press, 2020.","apa":"Paranjape, C. S., Duguet, Y., & Hof, B. (2020). Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.322","ama":"Paranjape CS, Duguet Y, Hof B. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 2020;897. doi:10.1017/jfm.2020.322","mla":"Paranjape, Chaitanya S., et al. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics, vol. 897, A7, Cambridge University Press, 2020, doi:10.1017/jfm.2020.322."},"title":"Oblique stripe solutions of channel flow","author":[{"first_name":"Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","full_name":"Paranjape, Chaitanya S","last_name":"Paranjape"},{"last_name":"Duguet","full_name":"Duguet, Yohann","first_name":"Yohann"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"external_id":{"isi":["000539132300001"]},"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","abstract":[{"lang":"eng","text":"With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain."}],"month":"08","intvolume":" 897","scopus_import":"1","file":[{"creator":"cziletti","file_size":767873,"date_updated":"2020-07-14T12:48:08Z","file_name":"2020_JournalOfFluidMech_Paranjape.pdf","date_created":"2020-06-30T08:37:37Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8070","checksum":"3f487bf6d9286787096306eaa18702e8"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14697645"],"issn":["00221120"]},"publication_status":"published","volume":897,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"8043","status":"public","article_type":"original","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"ddc":["530"],"date_updated":"2023-08-22T07:48:02Z","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:48:08Z"},{"doi":"10.1021/jacs.9b13450.s002","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8040"}]},"date_published":"2020-05-20T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2021-04-14T12:05:20Z","day":"20","year":"2020","month":"05","publisher":"American Chemical Society","main_file_link":[{"open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.","lang":"eng"}],"title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","department":[{"_id":"LeSa"}],"author":[{"first_name":"Chitrak","full_name":"Gupta, Chitrak","last_name":"Gupta"},{"first_name":"Umesh","full_name":"Khaniya, Umesh","last_name":"Khaniya"},{"full_name":"Chan, Chun","last_name":"Chan","first_name":"Chun"},{"last_name":"Dehez","full_name":"Dehez, Francois","first_name":"Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"last_name":"Gunner","full_name":"Gunner, M. R.","first_name":"M. R."},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"first_name":"Abhishek","last_name":"Singharoy","full_name":"Singharoy, Abhishek"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002."},"date_updated":"2023-08-22T07:49:37Z","status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"9326"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.04819","open_access":"1"}],"month":"07","intvolume":" 22","abstract":[{"text":"We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.","lang":"eng"}],"oa_version":"Preprint","volume":22,"issue":"7","publication_identifier":{"issn":["14359855"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"8042","department":[{"_id":"RoSe"}],"date_updated":"2023-08-22T07:47:04Z","publisher":"European Mathematical Society","quality_controlled":"1","oa":1,"page":"2331-2403","doi":"10.4171/JEMS/966","date_published":"2020-07-01T00:00:00Z","date_created":"2020-06-29T07:59:35Z","isi":1,"year":"2020","day":"01","publication":"Journal of the European Mathematical Society","author":[{"first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","last_name":"Boccato"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"article_processing_charge":"No","external_id":{"isi":["000548174700006"],"arxiv":["1704.04819"]},"title":"The excitation spectrum of Bose gases interacting through singular potentials","citation":{"short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403, 2020.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966","mla":"Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. European Mathematical Society, 2020. https://doi.org/10.4171/JEMS/966."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8093","department":[{"_id":"SiHi"}],"file_date_updated":"2021-12-02T12:35:12Z","date_updated":"2023-08-22T07:51:12Z","ddc":["610"],"scopus_import":"1","month":"09","intvolume":" 123","abstract":[{"lang":"eng","text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy."}],"pmid":1,"oa_version":"Published Version","volume":123,"related_material":{"record":[{"id":"10170","status":"deleted","relation":"later_version"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}]},"publication_identifier":{"eissn":["1532-1827"],"issn":["0007-0920"]},"publication_status":"published","file":[{"file_size":3620691,"date_updated":"2021-12-02T12:35:12Z","creator":"cchlebak","file_name":"2020_BrJournalCancer_Hippe.pdf","date_created":"2021-12-02T12:35:12Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","file_id":"10398"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Hippe, Andreas","last_name":"Hippe","first_name":"Andreas"},{"full_name":"Braun, Stephan Alexander","last_name":"Braun","first_name":"Stephan Alexander"},{"first_name":"Péter","full_name":"Oláh, Péter","last_name":"Oláh"},{"first_name":"Peter Arne","full_name":"Gerber, Peter Arne","last_name":"Gerber"},{"full_name":"Schorr, Anne","last_name":"Schorr","first_name":"Anne"},{"last_name":"Seeliger","full_name":"Seeliger, Stephan","first_name":"Stephan"},{"full_name":"Holtz, Stephanie","last_name":"Holtz","first_name":"Stephanie"},{"full_name":"Jannasch, Katharina","last_name":"Jannasch","first_name":"Katharina"},{"last_name":"Pivarcsi","full_name":"Pivarcsi, Andor","first_name":"Andor"},{"full_name":"Buhren, Bettina","last_name":"Buhren","first_name":"Bettina"},{"first_name":"Holger","full_name":"Schrumpf, Holger","last_name":"Schrumpf"},{"first_name":"Andreas","last_name":"Kislat","full_name":"Kislat, Andreas"},{"first_name":"Erich","full_name":"Bünemann, Erich","last_name":"Bünemann"},{"full_name":"Steinhoff, Martin","last_name":"Steinhoff","first_name":"Martin"},{"full_name":"Fischer, Jens","last_name":"Fischer","first_name":"Jens"},{"last_name":"Lira","full_name":"Lira, Sérgio A.","first_name":"Sérgio A."},{"last_name":"Boukamp","full_name":"Boukamp, Petra","first_name":"Petra"},{"last_name":"Hevezi","full_name":"Hevezi, Peter","first_name":"Peter"},{"last_name":"Stoecklein","full_name":"Stoecklein, Nikolas Hendrik","first_name":"Nikolas Hendrik"},{"full_name":"Hoffmann, Thomas","last_name":"Hoffmann","first_name":"Thomas"},{"first_name":"Frauke","last_name":"Alves","full_name":"Alves, Frauke"},{"first_name":"Jonathan","full_name":"Sleeman, Jonathan","last_name":"Sleeman"},{"full_name":"Bauer, Thomas","last_name":"Bauer","first_name":"Thomas"},{"first_name":"Jörg","full_name":"Klufa, Jörg","last_name":"Klufa"},{"last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"},{"first_name":"Albert","last_name":"Zlotnik","full_name":"Zlotnik, Albert"},{"last_name":"Müller-Homey","full_name":"Müller-Homey, Anja","first_name":"Anja"},{"full_name":"Homey, Bernhard","last_name":"Homey","first_name":"Bernhard"}],"article_processing_charge":"No","external_id":{"pmid":["32601464"],"isi":["000544152500001"]},"title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","citation":{"mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954.","ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.","ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","page":"942-954","doi":"10.1038/s41416-020-0943-2","date_published":"2020-09-15T00:00:00Z","date_created":"2020-07-05T22:00:46Z","isi":1,"has_accepted_license":"1","year":"2020","day":"15","publication":"British Journal of Cancer"},{"date_updated":"2023-08-22T07:51:47Z","ddc":["530"],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-11-25T15:05:04Z","_id":"8091","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"publication_status":"published","file":[{"checksum":"5cbeef52caf18d0d952f17fed7b5545a","file_id":"8812","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-11-25T15:05:04Z","file_name":"2020_JourStatPhysics_Seiringer.pdf","creator":"dernst","date_updated":"2020-11-25T15:05:04Z","file_size":404778}],"language":[{"iso":"eng"}],"volume":181,"ec_funded":1,"abstract":[{"text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"10","intvolume":" 181","citation":{"mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.","ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Jakob","last_name":"Yngvason","full_name":"Yngvason, Jakob"}],"external_id":{"isi":["000543030000002"],"arxiv":["2001.07144"]},"article_processing_charge":"Yes (via OA deal)","title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Statistical Physics","page":"448-464","date_published":"2020-10-01T00:00:00Z","doi":"10.1007/s10955-020-02586-0","date_created":"2020-07-05T22:00:46Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","quality_controlled":"1","publisher":"Springer","oa":1},{"acknowledgement":"The authors are grateful to the two anonymous referees for their insightful comments and suggestions which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013) (Grant agreement No. 616160).","publisher":"Elsevier","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Applied Numerical Mathematics","page":"315-337","doi":"10.1016/j.apnum.2020.06.009","date_published":"2020-11-01T00:00:00Z","date_created":"2020-07-02T09:02:33Z","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 157, 315–337.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009.","ama":"Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 2020;157:315-337. doi:10.1016/j.apnum.2020.06.009","apa":"Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009","ieee":"Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence,” Applied Numerical Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.","short":"Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Shehu","orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola"}],"article_processing_charge":"No","external_id":{"isi":["000564648400018"]},"title":"Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence","abstract":[{"lang":"eng","text":"The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods."}],"oa_version":"Submitted Version","scopus_import":"1","month":"11","intvolume":" 157","publication_identifier":{"issn":["0168-9274"]},"publication_status":"published","file":[{"date_created":"2020-07-02T09:08:59Z","file_name":"2020_AppliedNumericalMath_Shehu.pdf","date_updated":"2020-07-14T12:48:09Z","file_size":2874203,"creator":"dernst","file_id":"8078","checksum":"87d81324a62c82baa925c009dfcb0200","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":157,"ec_funded":1,"_id":"8077","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T07:50:43Z","ddc":["510"],"file_date_updated":"2020-07-14T12:48:09Z","department":[{"_id":"VlKo"}]},{"article_number":"60","citation":{"ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).","ieee":"R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1","mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos","first_name":"Daniel"},{"first_name":"Athanasios","full_name":"Kousathanas, Athanasios","last_name":"Kousathanas"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"last_name":"Stevenson","full_name":"Stevenson, Anna J.","first_name":"Anna J."},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"first_name":"Sven Erik","full_name":"Ojavee, Sven Erik","last_name":"Ojavee"},{"full_name":"Zhang, Qian","last_name":"Zhang","first_name":"Qian"},{"full_name":"Liewald, David C.","last_name":"Liewald","first_name":"David C."},{"first_name":"Craig W.","last_name":"Ritchie","full_name":"Ritchie, Craig W."},{"last_name":"Evans","full_name":"Evans, Kathryn L.","first_name":"Kathryn L."},{"last_name":"Tucker-Drob","full_name":"Tucker-Drob, Elliot M.","first_name":"Elliot M."},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"first_name":"Allan F.","last_name":"Mcrae","full_name":"Mcrae, Allan F."},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"first_name":"Riccardo E.","full_name":"Marioni, Riccardo E.","last_name":"Marioni"}],"external_id":{"pmid":["32641083"],"isi":["000551778400001"]},"article_processing_charge":"No","title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"08","publication":"Genome Medicine","doi":"10.1186/s13073-020-00754-1","date_published":"2020-07-08T00:00:00Z","date_created":"2020-07-19T22:00:58Z","_id":"8133","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-22T07:55:37Z","ddc":["570"],"file_date_updated":"2020-07-22T06:27:38Z","department":[{"_id":"MaRo"}],"abstract":[{"text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"07","intvolume":" 12","publication_identifier":{"eissn":["1756994X"]},"publication_status":"published","file":[{"date_created":"2020-07-22T06:27:38Z","file_name":"2020_GenomeMedicine_Hillary.pdf","creator":"dernst","date_updated":"2020-07-22T06:27:38Z","file_size":1136983,"file_id":"8145","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"9706","status":"public"}]},"issue":"1","volume":12},{"citation":{"apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261.","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32940606"],"isi":["000584989400001"]},"article_processing_charge":"No","author":[{"first_name":"Pedro J.","full_name":"Gonçalves, Pedro J.","orcid":"0000-0002-6987-4836","last_name":"Gonçalves"},{"first_name":"Jan-Matthis","orcid":"0000-0003-4320-4663","full_name":"Lueckmann, Jan-Matthis","last_name":"Lueckmann"},{"full_name":"Deistler, Michael","orcid":"0000-0002-3573-0404","last_name":"Deistler","first_name":"Michael"},{"first_name":"Marcel","orcid":"0000-0001-6044-6627","full_name":"Nonnenmacher, Marcel","last_name":"Nonnenmacher"},{"first_name":"Kaan","last_name":"Öcal","orcid":"0000-0002-8528-6858","full_name":"Öcal, Kaan"},{"first_name":"Giacomo","last_name":"Bassetto","full_name":"Bassetto, Giacomo"},{"first_name":"Chaitanya","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya","orcid":"0000-0003-4252-1608","last_name":"Chintaluri"},{"last_name":"Podlaski","full_name":"Podlaski, William F.","orcid":"0000-0001-6619-7502","first_name":"William F."},{"first_name":"Sara A.","full_name":"Haddad, Sara A.","orcid":"0000-0003-0807-0823","last_name":"Haddad"},{"last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"David S.","full_name":"Greenberg, David S.","last_name":"Greenberg"},{"last_name":"Macke","full_name":"Macke, Jakob H.","orcid":"0000-0001-5154-8912","first_name":"Jakob H."}],"title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","article_number":"e56261","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"17","date_created":"2020-07-16T12:26:04Z","date_published":"2020-09-17T00:00:00Z","doi":"10.7554/eLife.56261","acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_updated":"2023-08-22T07:54:52Z","ddc":["570"],"department":[{"_id":"TiVo"}],"file_date_updated":"2020-10-27T11:37:32Z","_id":"8127","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8709","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_eLife_Gonçalves.pdf","date_created":"2020-10-27T11:37:32Z","creator":"cziletti","file_size":17355867,"date_updated":"2020-10-27T11:37:32Z"}],"ec_funded":1,"volume":9,"abstract":[{"text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"09"},{"title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","author":[{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J.","orcid":"0000-0001-7184-7311"},{"last_name":"Luppi","full_name":"Luppi, Andrea I.","first_name":"Andrea I."},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"article_processing_charge":"No","external_id":{"pmid":["33168622"],"isi":["000606706400009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.","short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020."},"date_published":"2020-12-09T00:00:00Z","doi":"10.1523/JNEUROSCI.0276-20.2020","date_created":"2020-07-16T12:25:04Z","page":"9634-9649","day":"09","publication":"The Journal of Neuroscience","isi":1,"has_accepted_license":"1","year":"2020","publisher":"Society for Neuroscience","quality_controlled":"1","oa":1,"department":[{"_id":"TiVo"}],"file_date_updated":"2020-12-28T08:31:47Z","ddc":["570"],"date_updated":"2023-08-22T07:54:26Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8126","issue":"50","volume":40,"file":[{"file_name":"2020_JourNeuroscience_Agnes.pdf","date_created":"2020-12-28T08:31:47Z","file_size":2750920,"date_updated":"2020-12-28T08:31:47Z","creator":"dernst","success":1,"file_id":"8977","checksum":"7977e4dd6b89357d1a5cc88babac56da","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2401"]},"publication_status":"published","month":"12","intvolume":" 40","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.","lang":"eng"}]},{"date_updated":"2023-08-22T07:55:36Z","citation":{"ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Hillary","full_name":"Hillary, Robert F.","first_name":"Robert F."},{"last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel","first_name":"Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"full_name":"McCartney, Daniel L.","last_name":"McCartney","first_name":"Daniel L."},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"last_name":"Stevenson","full_name":"Stevenson, Anna J.","first_name":"Anna J."},{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"first_name":"Sven Erik","last_name":"Ojavee","full_name":"Ojavee, Sven Erik"},{"full_name":"Zhang, Qian","last_name":"Zhang","first_name":"Qian"},{"full_name":"Liewald, David C.","last_name":"Liewald","first_name":"David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"full_name":"Evans, Kathryn L.","last_name":"Evans","first_name":"Kathryn L."},{"first_name":"Elliot M.","full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob"},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"first_name":"Allan F. ","last_name":"McRae","full_name":"McRae, Allan F. "},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."},{"first_name":"Ian J.","full_name":"Deary, Ian J.","last_name":"Deary"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"},{"first_name":"Riccardo E. ","last_name":"Marioni","full_name":"Marioni, Riccardo E. "}],"article_processing_charge":"No","department":[{"_id":"MaRo"}],"title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","_id":"9706","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2020","day":"09","date_published":"2020-07-09T00:00:00Z","doi":"10.6084/m9.figshare.12629697.v1","related_material":{"record":[{"relation":"used_in_publication","id":"8133","status":"public"}]},"date_created":"2021-07-23T08:59:15Z","abstract":[{"text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).","lang":"eng"}],"oa_version":"Published Version","publisher":"Springer Nature","oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"month":"07","other_data_license":"CC0 + CC BY (4.0)"},{"department":[{"_id":"RoSe"}],"date_updated":"2023-08-22T08:12:40Z","status":"public","article_type":"original","type":"journal_article","_id":"8134","ec_funded":1,"issue":"6","volume":61,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00222488"]},"intvolume":" 61","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion."}],"title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","external_id":{"isi":["000544595100001"],"arxiv":["2002.08281"]},"article_processing_charge":"No","author":[{"first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon","last_name":"Mayer"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950.","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901."},"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_number":"061901","date_created":"2020-07-19T22:00:59Z","date_published":"2020-06-22T00:00:00Z","doi":"10.1063/5.0005950","publication":"Journal of Mathematical Physics","day":"22","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"AIP Publishing"},{"department":[{"_id":"SiHi"}],"file_date_updated":"2020-12-02T09:26:46Z","ddc":["570"],"date_updated":"2023-08-22T08:20:11Z","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"8162","issue":"6","volume":107,"related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/","relation":"press_release"}]},"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-12-02T09:26:46Z","file_size":8911830,"date_created":"2020-12-02T09:26:46Z","file_name":"2020_Neuron_Laukoter.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7becdc16a6317304304631087ae7dd7f","file_id":"8828","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","month":"09","intvolume":" 107","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"title":"Cell-type specificity of genomic imprinting in cerebral cortex","author":[{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","last_name":"Beattie","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753"},{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Penz, Thomas","last_name":"Penz","first_name":"Thomas"},{"first_name":"Christoph","last_name":"Bock","orcid":"0000-0001-6091-3088","full_name":"Bock, Christoph"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"article_processing_charge":"No","external_id":{"isi":["000579698700006"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031","ieee":"S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031."},"project":[{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1016/j.neuron.2020.06.031","date_published":"2020-09-23T00:00:00Z","date_created":"2020-07-23T16:03:12Z","page":"1160-1179.e9","day":"23","publication":"Neuron","has_accepted_license":"1","isi":1,"year":"2020","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H."},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8138","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-22T08:32:55Z","date_updated":"2023-08-22T08:13:44Z","ddc":["580"],"scopus_import":"1","intvolume":" 11","month":"07","abstract":[{"text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"ec_funded":1,"related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"}]},"issue":"1","volume":11,"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8148","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-22T08:32:55Z","file_name":"2020_NatureComm_Zhang.pdf","creator":"dernst","date_updated":"2020-07-22T08:32:55Z","file_size":1759490}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"pmid":["32665554"],"isi":["000550062200004"]},"author":[{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"first_name":"E","full_name":"Mazur, E","last_name":"Mazur"},{"full_name":"Balla, J","last_name":"Balla","first_name":"J"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"full_name":"Kalousek, P","last_name":"Kalousek","first_name":"P"},{"first_name":"Z","last_name":"Medveďová","full_name":"Medveďová, Z"},{"first_name":"Y","full_name":"Li, Y","last_name":"Li"},{"full_name":"Wang, Y","last_name":"Wang","first_name":"Y"},{"full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vasileva, Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K"},{"last_name":"Reinöhl","full_name":"Reinöhl, V","first_name":"V"},{"full_name":"Procházka, S","last_name":"Procházka","first_name":"S"},{"first_name":"R","full_name":"Halouzka, R","last_name":"Halouzka"},{"first_name":"P","full_name":"Tarkowski, P","last_name":"Tarkowski"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"},{"first_name":"PB","full_name":"Brewer, PB","last_name":"Brewer"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","citation":{"apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y","short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","ieee":"J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","page":"3508","date_created":"2020-07-21T08:58:07Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1038/s41467-020-17252-y","year":"2020","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"14"},{"abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"month":"07","intvolume":" 375","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":375,"issue":"1806","ec_funded":1,"_id":"8168","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T08:21:31Z","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","doi":"10.1098/rstb.2019.0528","date_published":"2020-07-12T00:00:00Z","date_created":"2020-07-26T22:01:01Z","article_number":"20190528","project":[{"call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"citation":{"mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Jonna","full_name":"Kulmuni, Jonna","last_name":"Kulmuni"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Kay","last_name":"Lucek","full_name":"Lucek, Kay"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"}],"article_processing_charge":"No","external_id":{"pmid":["32654637"],"isi":["000552662100001"]},"title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers"},{"article_number":"20190545","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka"},{"first_name":"Isobel","full_name":"Eyres, Isobel","last_name":"Eyres"},{"first_name":"Thomas","last_name":"Broquet","full_name":"Broquet, Thomas"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"article_processing_charge":"No","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","citation":{"mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"The Royal Society","quality_controlled":"1","oa":1,"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","date_published":"2020-07-12T00:00:00Z","doi":"10.1098/rstb.2019.0545","date_created":"2020-07-26T22:01:01Z","isi":1,"year":"2020","day":"12","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","article_type":"original","type":"journal_article","status":"public","_id":"8167","department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T08:22:13Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0545"}],"month":"07","intvolume":" 375","abstract":[{"text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"1806","volume":375,"publication_identifier":{"eissn":["1471-2970"]},"publication_status":"published","language":[{"iso":"eng"}]},{"_id":"8170","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-22T08:22:43Z","department":[{"_id":"MiLe"}],"abstract":[{"text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.02694"}],"month":"07","intvolume":" 125","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":125,"ec_funded":1,"article_number":"013001","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"A path-integral approach to composite impurities","grant_number":"M02641"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"citation":{"chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ieee":"A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Chatterley","full_name":"Chatterley, Adam S.","first_name":"Adam S."},{"first_name":"Lars","full_name":"Christiansen, Lars","last_name":"Christiansen"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"first_name":"Anders V.","last_name":"Jørgensen","full_name":"Jørgensen, Anders V."},{"first_name":"Benjamin","full_name":"Shepperson, Benjamin","last_name":"Shepperson"},{"full_name":"Cherepanov, Igor","last_name":"Cherepanov","first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"full_name":"Zillich, Robert E.","last_name":"Zillich","first_name":"Robert E."},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"}],"external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"article_processing_charge":"No","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2020","day":"03","publication":"Physical Review Letters","date_published":"2020-07-03T00:00:00Z","doi":"10.1103/PhysRevLett.125.013001","date_created":"2020-07-26T22:01:02Z"},{"department":[{"_id":"ToHe"}],"date_updated":"2023-08-22T08:27:25Z","status":"public","conference":{"name":"IJCAR: International Joint Conference on Automated Reasoning","start_date":"2020-07-01","end_date":"2020-07-04","location":"Paris, France"},"type":"conference","_id":"8194","volume":12166,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030510732"],"eissn":["16113349"],"issn":["03029743"]},"intvolume":" 12166","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.","lang":"eng"}],"title":"An SMT theory of fixed-point arithmetic","article_processing_charge":"No","external_id":{"isi":["000884318000002"]},"author":[{"last_name":"Baranowski","full_name":"Baranowski, Marek","first_name":"Marek"},{"first_name":"Shaobo","last_name":"He","full_name":"He, Shaobo"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thanh Son","full_name":"Nguyen, Thanh Son","last_name":"Nguyen"},{"full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić","first_name":"Zvonimir"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2.","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31."},"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2020-08-02T22:00:59Z","doi":"10.1007/978-3-030-51074-9_2","date_published":"2020-06-24T00:00:00Z","page":"13-31","publication":"Automated Reasoning","day":"24","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"_id":"8220","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-22T08:29:30Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2020-08-10T06:50:28Z","abstract":[{"lang":"eng","text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 117","month":"07","publication_status":"published","publication_identifier":{"eissn":["10916490"]},"language":[{"iso":"eng"}],"file":[{"file_size":1111604,"date_updated":"2020-08-10T06:50:28Z","creator":"dernst","file_name":"2020_PNAS_Corominas.pdf","date_created":"2020-08-10T06:50:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8223"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"volume":117,"issue":"29","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"citation":{"ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"first_name":"Saskia I.J.","last_name":"Ellenbroek","full_name":"Ellenbroek, Saskia I.J."},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"first_name":"Jacco","full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"title":"Stem cell lineage survival as a noisy competition for niche access","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2020","has_accepted_license":"1","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"21","page":"16969-16975","date_created":"2020-08-09T22:00:52Z","doi":"10.1073/pnas.1921205117","date_published":"2020-07-21T00:00:00Z"},{"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","author":[{"first_name":"Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","full_name":"Gulden, Tobias","orcid":"0000-0001-6814-7541","last_name":"Gulden"},{"first_name":"Erez","full_name":"Berg, Erez","last_name":"Berg"},{"first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer","last_name":"Rudner"},{"last_name":"Lindner","full_name":"Lindner, Netanel","first_name":"Netanel"}],"article_processing_charge":"No","external_id":{"isi":["000557362300008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020.","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"015","date_published":"2020-07-29T00:00:00Z","doi":"10.21468/scipostphys.9.1.015","date_created":"2020-08-04T13:04:15Z","day":"29","publication":"SciPost Physics","isi":1,"has_accepted_license":"1","year":"2020","publisher":"SciPost Foundation","quality_controlled":"1","oa":1,"acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","department":[{"_id":"MaSe"}],"file_date_updated":"2020-08-06T08:56:06Z","ddc":["530"],"date_updated":"2023-08-22T08:28:24Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8199","volume":9,"ec_funded":1,"file":[{"file_name":"2020_SciPostPhys_Gulden.pdf","date_created":"2020-08-06T08:56:06Z","creator":"dernst","file_size":531137,"date_updated":"2020-08-06T08:56:06Z","success":1,"file_id":"8202","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2542-4653"]},"publication_status":"published","month":"07","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}]},{"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"abstract":[{"text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.","lang":"eng"}],"month":"09","intvolume":" 107","file":[{"date_updated":"2020-12-04T09:29:21Z","file_size":3011120,"creator":"dernst","date_created":"2020-12-04T09:29:21Z","file_name":"2020_Neuron_Zhang.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"44a5960fc083a4cb3488d22224859fdc","file_id":"8920","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"publication_status":"published","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/"}]},"volume":107,"issue":"6","ec_funded":1,"_id":"8261","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2023-08-22T08:30:55Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"file_date_updated":"2020-12-04T09:29:21Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"23","publication":"Neuron","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-09-23T00:00:00Z","doi":"10.1016/j.neuron.2020.07.006","date_created":"2020-08-14T09:36:05Z","page":"1212-1225","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006."},"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","author":[{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000579698700009"],"pmid":["32763145"]}},{"date_created":"2020-08-16T22:00:56Z","doi":"10.1109/TSP.2020.3010355","date_published":"2020-07-20T00:00:00Z","page":"4268-4282","publication":"IEEE Transactions on Signal Processing","day":"20","year":"2020","isi":1,"oa":1,"publisher":"IEEE","quality_controlled":"1","acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"article_processing_charge":"No","author":[{"full_name":"Gurel, Nezihe Merve","last_name":"Gurel","first_name":"Nezihe Merve"},{"last_name":"Kara","full_name":"Kara, Kaan","first_name":"Kaan"},{"first_name":"Alen","full_name":"Stojanov, Alen","last_name":"Stojanov"},{"first_name":"Tyler","last_name":"Smith","full_name":"Smith, Tyler"},{"first_name":"Thomas","full_name":"Lemmin, Thomas","last_name":"Lemmin"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Markus","full_name":"Puschel, Markus","last_name":"Puschel"},{"last_name":"Zhang","full_name":"Zhang, Ce","first_name":"Ce"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","ieee":"N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.","chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282."},"volume":68,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1053587X"],"eissn":["19410476"]},"intvolume":" 68","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"department":[{"_id":"DaAl"}],"date_updated":"2023-08-22T08:40:08Z","status":"public","type":"journal_article","article_type":"original","_id":"8268"},{"article_number":"082602","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602.","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602.","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","last_name":"Grosjean"},{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","full_name":"Wald, Sebastian","last_name":"Wald"},{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2006.07120"],"isi":["000561897000001"]},"article_processing_charge":"Yes","title":"Quantitatively consistent scale-spanning model for same-material tribocharging","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"17","publication":"Physical Review Materials","date_published":"2020-08-17T00:00:00Z","doi":"10.1103/PhysRevMaterials.4.082602","date_created":"2020-07-07T11:33:54Z","_id":"8101","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"date_updated":"2023-08-22T08:41:32Z","ddc":["530"],"file_date_updated":"2020-08-17T15:54:20Z","department":[{"_id":"ScWa"}],"abstract":[{"lang":"eng","text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature."}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 4","publication_identifier":{"issn":["2475-9953"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","file_id":"8277","success":1,"date_updated":"2020-08-17T15:54:20Z","file_size":853753,"creator":"ggrosjea","date_created":"2020-08-17T15:54:20Z","file_name":"Grosjean2020.pdf"}],"language":[{"iso":"eng"}],"issue":"8","related_material":{"record":[{"status":"public","id":"12697","relation":"popular_science"}]},"volume":4,"ec_funded":1},{"ec_funded":1,"volume":378,"issue":"9","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"intvolume":" 378","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. ","lang":"eng"}],"department":[{"_id":"TaHa"}],"date_updated":"2023-08-22T09:00:03Z","status":"public","type":"journal_article","article_type":"original","_id":"8325","date_created":"2020-08-30T22:01:13Z","date_published":"2020-09-01T00:00:00Z","doi":"10.1007/s00220-020-03828-8","page":"1649-1675","publication":"Communications in Mathematical Physics","day":"01","year":"2020","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","title":"Sandpile solitons via smoothing of superharmonic functions","article_processing_charge":"No","external_id":{"isi":["000560620600001"],"arxiv":["1711.04285"]},"author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8","apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675."},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"date_updated":"2023-08-22T09:03:00Z","ddc":["570"],"file_date_updated":"2020-08-31T13:40:00Z","department":[{"_id":"LeSa"}],"_id":"8318","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"52b96f41d7d0db9728064c08da00d030","file_id":"8326","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","date_created":"2020-08-31T13:40:00Z","creator":"cziletti","file_size":7527373,"date_updated":"2020-08-31T13:40:00Z"}],"issue":"1","volume":11,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"abstract":[{"lang":"eng","text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"08","citation":{"ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"article_processing_charge":"No","author":[{"first_name":"Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gurdeep S.","last_name":"Minhas","full_name":"Minhas, Gurdeep S."},{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh"},{"first_name":"Margherita","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","full_name":"Tambalo, Margherita"},{"first_name":"David T.","full_name":"Gallagher, David T.","last_name":"Gallagher"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"title":"Key role of quinone in the mechanism of respiratory complex I","article_number":"4135","year":"2020","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"18","date_created":"2020-08-30T22:01:10Z","doi":"10.1038/s41467-020-17957-0","date_published":"2020-08-18T00:00:00Z","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"citation":{"ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000561483500001"]},"article_processing_charge":"No","author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"title":"A farewell to Ricky Pollack","oa":1,"publisher":"Springer Nature","year":"2020","isi":1,"publication":"Discrete and Computational Geometry","day":"01","page":"571-574","date_created":"2020-08-30T22:01:12Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1007/s00454-020-00237-5","_id":"8323","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-08-22T09:05:04Z","department":[{"_id":"HeEd"}],"oa_version":"None","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"scopus_import":"1","intvolume":" 64","month":"10","publication_status":"published","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"language":[{"iso":"eng"}],"volume":64},{"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","file_id":"8357","success":1,"creator":"dernst","date_updated":"2020-09-10T08:05:19Z","file_size":3455704,"date_created":"2020-09-10T08:05:19Z","file_name":"2020_NatureComm_Kubiasova.pdf"}],"language":[{"iso":"eng"}],"volume":11,"ec_funded":1,"abstract":[{"lang":"eng","text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 11","date_updated":"2023-08-22T09:09:06Z","ddc":["580"],"file_date_updated":"2020-09-10T08:05:19Z","department":[{"_id":"EvBe"}],"_id":"8336","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2020","day":"27","publication":"Nature Communications","date_published":"2020-08-27T00:00:00Z","doi":"10.1038/s41467-020-17949-0","date_created":"2020-09-06T22:01:12Z","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"946011F4-3E71-11EA-860B-C7A73DDC885E","first_name":"Karolina","last_name":"Kubiasova","orcid":"0000-0001-5630-9419","full_name":"Kubiasova, Karolina"},{"first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"full_name":"Šamajová, Olga","last_name":"Šamajová","first_name":"Olga"},{"last_name":"Nisler","full_name":"Nisler, Jaroslav","first_name":"Jaroslav"},{"last_name":"Mik","full_name":"Mik, Václav","first_name":"Václav"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Plíhalová","full_name":"Plíhalová, Lucie","first_name":"Lucie"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavý","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter"},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"},{"first_name":"Karel","full_name":"Berka, Karel","last_name":"Berka"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"full_name":"Galuszka, Petr","last_name":"Galuszka","first_name":"Petr"},{"first_name":"Jozef","full_name":"Šamaj, Jozef","last_name":"Šamaj"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"first_name":"Ondřej","full_name":"Plíhal, Ondřej","last_name":"Plíhal"},{"full_name":"Spíchal, Lukáš","last_name":"Spíchal","first_name":"Lukáš"}],"article_processing_charge":"No","external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","article_number":"4285","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."},{"grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}]}]