[{"issue":"6","date_published":"2018-05-18T00:00:00Z","abstract":[{"lang":"eng","text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux."}],"volume":19,"author":[{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","full_name":"Hons, Miroslav","last_name":"Hons","first_name":"Miroslav","orcid":"0000-0002-6625-3348"},{"orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja"},{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R","last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stein, Jens","last_name":"Stein","first_name":"Jens"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"year":"2018","language":[{"iso":"eng"}],"day":"18","publication":"Nature Immunology","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"pmid":1,"publisher":"Nature Publishing Group","scopus_import":"1","date_created":"2018-12-11T11:44:10Z","project":[{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients"},{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","grant_number":"281556"}],"related_material":{"record":[{"status":"public","id":"6891","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8040","oa_version":"Published Version","month":"05","date_updated":"2024-03-25T23:30:22Z","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"isi":1,"citation":{"ieee":"M. Hons <i>et al.</i>, “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” <i>Nature Immunology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. 2018;19(6):606-616. doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>.","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>"},"article_processing_charge":"No","status":"public","type":"journal_article","title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","intvolume":"        19","page":"606 - 616","_id":"15","external_id":{"isi":["000433041500026"],"pmid":["29777221"]},"doi":"10.1038/s41590-018-0109-z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"quality_controlled":"1","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014)."},{"article_type":"original","date_created":"2018-12-11T11:44:53Z","scopus_import":"1","publisher":"Nature Publishing Group","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"publication":"Nature","day":"29","language":[{"iso":"eng"}],"year":"2018","author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"last_name":"Zadrozny","first_name":"Kaneil K","full_name":"Zadrozny, Kaneil K"},{"last_name":"Xu","first_name":"Chaoyi","full_name":"Xu, Chaoyi"},{"first_name":"Florian","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian"},{"last_name":"Lyddon","first_name":"Terri D","full_name":"Lyddon, Terri D"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"first_name":"Jonathan M","last_name":"Wagner","full_name":"Wagner, Jonathan M"},{"first_name":"Juan R","last_name":"Perilla","full_name":"Perilla, Juan R"},{"first_name":"Pornillos Barbie K","last_name":"Ganser","full_name":"Ganser, Pornillos Barbie K"},{"full_name":"Johnson, Marc C","last_name":"Johnson","first_name":"Marc C"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"volume":560,"abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"date_published":"2018-08-29T00:00:00Z","issue":"7719","quality_controlled":"1","department":[{"_id":"FlSc"}],"doi":"10.1038/s41586-018-0396-4","external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"_id":"150","page":"509–512","intvolume":"       560","title":"Inositol phosphates are assembly co-factors for HIV-1","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018."},"isi":1,"publication_status":"published","oa":1,"date_updated":"2023-09-12T07:44:37Z","publication_identifier":{"eissn":["1476-4687"]},"month":"08","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]}},{"intvolume":"        28","_id":"152","page":"835 - 867","external_id":{"isi":["000445118200007"]},"doi":"10.1016/j.tcb.2018.06.006","department":[{"_id":"LeSa"}],"quality_controlled":"1","isi":1,"citation":{"apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018."},"article_processing_charge":"No","status":"public","type":"journal_article","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Mammalian mitochondrial complex I structure and disease causing mutations","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7769","oa_version":"Submitted Version","month":"07","date_updated":"2023-09-13T08:51:56Z","ddc":["572"],"publication_status":"published","oa":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:54Z","article_type":"original","file":[{"checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","creator":"lsazanov","date_created":"2019-11-07T12:55:20Z","file_id":"6994","access_level":"open_access","file_size":2185385,"file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z"}],"publisher":"Elsevier","scopus_import":"1","year":"2018","language":[{"iso":"eng"}],"day":"26","publication":"Trends in Cell Biology","issue":"10","file_date_updated":"2020-07-14T12:45:00Z","date_published":"2018-07-26T00:00:00Z","abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"volume":28,"author":[{"full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","last_name":"Fiedorczuk","first_name":"Karol"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}]},{"type":"book_chapter","status":"public","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","isi":1,"citation":{"ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>."},"article_processing_charge":"No","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"quality_controlled":"1","page":"79 - 91","_id":"153","intvolume":"       147","doi":"10.1016/bs.mcb.2018.07.004","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"date_updated":"2023-09-13T08:56:35Z","publication_identifier":{"issn":["0091679X"]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7768","month":"07","oa_version":"None","scopus_import":"1","publisher":"Academic Press","pmid":1,"date_created":"2018-12-11T11:44:54Z","abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"volume":147,"date_published":"2018-07-27T00:00:00Z","author":[{"orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","last_name":"Reversat","first_name":"Anne"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner","first_name":"Alexander F"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"day":"27","language":[{"iso":"eng"}],"year":"2018","publication":"Methods in Cell Biology"},{"publisher":"Springer","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","file_size":496973,"file_name":"2018_MathPhysics_Moser.pdf","file_id":"5729","relation":"main_file","checksum":"411c4db5700d7297c9cd8ebc5dd29091","creator":"dernst","date_created":"2018-12-17T16:49:02Z"}],"scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"},{"call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"date_created":"2018-12-11T11:44:55Z","article_type":"original","file_date_updated":"2020-07-14T12:45:01Z","issue":"3","author":[{"last_name":"Moser","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-09-01T00:00:00Z","volume":21,"abstract":[{"text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system.","lang":"eng"}],"publication":"Mathematical Physics Analysis and Geometry","year":"2018","language":[{"iso":"eng"}],"day":"01","ec_funded":1,"article_processing_charge":"No","citation":{"mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3, 19, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>.","apa":"Moser, T., &#38; Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. 2018;21(3). doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19.","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3. Springer, 2018."},"isi":1,"tmp":{"short":"CC BY (4.0)","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)"},"title":"Stability of the 2+2 fermionic system with point interactions","type":"journal_article","status":"public","external_id":{"isi":["000439639700001"]},"doi":"10.1007/s11040-018-9275-3","intvolume":"        21","_id":"154","quality_controlled":"1","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","department":[{"_id":"RoSe"}],"has_accepted_license":"1","article_number":"19","oa_version":"Published Version","month":"09","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"52"}]},"publist_id":"7767","publication_status":"published","oa":1,"publication_identifier":{"eissn":["15729656"],"issn":["13850172"]},"date_updated":"2023-09-19T09:31:15Z","ddc":["530"]},{"publist_id":"7766","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"05","date_updated":"2023-09-18T08:12:24Z","conference":{"name":"SPIE: The international society for optical engineering","end_date":"2018-04-26","start_date":"2018-04-22","location":"Strasbourg, France"},"oa":1,"publication_status":"published","alternative_title":["Proceedings of SPIE"],"arxiv":1,"article_number":"106721N","intvolume":"     10672","_id":"155","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"doi":"10.1117/12.2309928","editor":[{"first_name":"D L","last_name":"Andrews","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","first_name":"A","last_name":"Ostendorf"},{"full_name":"Bain, A J","last_name":"Bain","first_name":"A J"},{"full_name":"Nunzi, J M","last_name":"Nunzi","first_name":"J M"}],"department":[{"_id":"JoFi"}],"quality_controlled":"1","isi":1,"article_processing_charge":"No","citation":{"mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N."},"status":"public","type":"conference","title":"Routing thermal noise through quantum networks","language":[{"iso":"eng"}],"year":"2018","day":"04","date_published":"2018-05-04T00:00:00Z","abstract":[{"lang":"eng","text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource."}],"volume":10672,"author":[{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","first_name":"Shabir"}],"date_created":"2018-12-11T11:44:55Z","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"publisher":"SPIE","scopus_import":"1"},{"file_date_updated":"2020-10-09T06:22:41Z","abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}],"volume":10951,"date_published":"2018-07-12T00:00:00Z","author":[{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"}],"day":"12","year":"2018","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_size":485576,"file_name":"2018_LNCS_Ferrere.pdf","content_type":"application/pdf","date_updated":"2020-10-09T06:22:41Z","relation":"main_file","checksum":"a045c213c42c445f1889326f8db82a0a","date_created":"2020-10-09T06:22:41Z","creator":"dernst","file_id":"8637","success":1}],"publisher":"Springer","scopus_import":"1","date_created":"2018-12-11T11:44:55Z","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"}],"alternative_title":["LNCS"],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7765","month":"07","oa_version":"Submitted Version","ddc":["000"],"date_updated":"2023-09-19T10:05:37Z","oa":1,"publication_status":"published","conference":{"name":"FM: International Symposium on Formal Methods","start_date":"2018-07-15","end_date":"2018-07-17","location":"Oxford, UK"},"isi":1,"article_processing_charge":"No","citation":{"short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164."},"status":"public","type":"conference","title":"The compound interest in relaxing punctuality","_id":"156","page":"147 - 164","intvolume":"     10951","doi":"10.1007/978-3-319-95582-7_9","external_id":{"isi":["000489765800009"]},"department":[{"_id":"ToHe"}],"quality_controlled":"1"},{"title":"Evolution of cooperation in stochastic games","type":"journal_article","status":"public","article_processing_charge":"No","citation":{"ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>"},"isi":1,"quality_controlled":"1","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","department":[{"_id":"KrCh"}],"external_id":{"isi":["000438240900054"]},"doi":"10.1038/s41586-018-0277-x","intvolume":"       559","page":"246 - 249","_id":"157","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["000"],"date_updated":"2023-09-11T13:43:22Z","oa_version":"Submitted Version","month":"07","publist_id":"7764","related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage","relation":"press_release"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publisher":"Nature Publishing Group","file":[{"file_id":"7049","date_created":"2019-11-19T08:09:57Z","creator":"dernst","relation":"main_file","checksum":"011ab905cf9a410bc2b96f15174d654d","date_updated":"2020-07-14T12:45:02Z","content_type":"application/pdf","file_name":"2018_Nature_Hilbe.pdf","access_level":"open_access","file_size":2834442}],"date_created":"2018-12-11T11:44:56Z","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"first_name":"Štepán","last_name":"Šimsa","full_name":"Šimsa, Štepán"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"date_published":"2018-07-04T00:00:00Z","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"volume":559,"file_date_updated":"2020-07-14T12:45:02Z","issue":"7713","ec_funded":1,"publication":"Nature","year":"2018","language":[{"iso":"eng"}],"day":"04"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"pmid":1,"publisher":"Nature Publishing Group","scopus_import":"1","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"date_created":"2018-12-11T11:44:56Z","issue":"8","author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Park, Chulmin","first_name":"Chulmin","last_name":"Park"},{"full_name":"Gutièrrez, Carla","first_name":"Carla","last_name":"Gutièrrez"},{"full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska","first_name":"Barbara"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Chen, Junyi","first_name":"Junyi","last_name":"Chen"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"full_name":"Laux, Thomas","first_name":"Thomas","last_name":"Laux"}],"date_published":"2018-07-16T00:00:00Z","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"volume":4,"publication":"Nature Plants","language":[{"iso":"eng"}],"year":"2018","day":"16","ec_funded":1,"citation":{"ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>."},"article_processing_charge":"No","isi":1,"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","type":"journal_article","status":"public","external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"doi":"10.1038/s41477-018-0204-z","intvolume":"         4","page":"548 - 553","_id":"158","quality_controlled":"1","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","department":[{"_id":"JiFr"}],"month":"07","oa_version":"Submitted Version","publist_id":"7763","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","oa":1,"date_updated":"2025-05-07T11:12:31Z"},{"department":[{"_id":"JoDa"}],"quality_controlled":"1","page":"764 - 767","_id":"159","intvolume":"        14","doi":"10.1038/s41589-018-0090-8","external_id":{"isi":["000438970200010"]},"type":"journal_article","status":"public","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","isi":1,"article_processing_charge":"No","citation":{"ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","ieee":"T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767. doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>."},"ddc":["570"],"date_updated":"2023-09-13T09:36:35Z","publication_status":"published","oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41589-021-00744-3"}]},"publist_id":"7762","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","oa_version":"Submitted Version","has_accepted_license":"1","date_created":"2018-12-11T11:44:56Z","article_type":"original","scopus_import":"1","file":[{"relation":"main_file","checksum":"d42935094ec845f54a0688bf12986d62","creator":"dernst","date_created":"2020-05-14T12:14:09Z","file_id":"7832","file_size":6321000,"access_level":"open_access","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:03Z"}],"publisher":"Nature Publishing Group","day":"16","year":"2018","language":[{"iso":"eng"}],"publication":"Nature Chemical Biology","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"volume":14,"date_published":"2018-07-16T00:00:00Z","author":[{"full_name":"Fehrentz, Timm","last_name":"Fehrentz","first_name":"Timm"},{"first_name":"Florian","last_name":"Huber","full_name":"Huber, Florian"},{"last_name":"Hartrampf","first_name":"Nina","full_name":"Hartrampf, Nina"},{"full_name":"Bruegmann, Tobias","last_name":"Bruegmann","first_name":"Tobias"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"last_name":"Fine","first_name":"Nicholas","full_name":"Fine, Nicholas"},{"first_name":"Daniela","last_name":"Malan","full_name":"Malan, Daniela"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"first_name":"Maritn","last_name":"Sumser","full_name":"Sumser, Maritn"},{"last_name":"Sasse","first_name":"Philipp","full_name":"Sasse, Philipp"},{"full_name":"Hodson, David","first_name":"David","last_name":"Hodson"},{"full_name":"Zhorov, Boris","last_name":"Zhorov","first_name":"Boris"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"first_name":"Dirk","last_name":"Trauner","full_name":"Trauner, Dirk"}],"issue":"8","file_date_updated":"2020-07-14T12:45:03Z"},{"oa_version":"Submitted Version","month":"10","publist_id":"8039","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","oa":1,"date_updated":"2023-09-13T08:57:05Z","ddc":["532"],"has_accepted_license":"1","article_number":"103303","external_id":{"isi":["000447469200001"]},"doi":"10.1103/PhysRevFluids.3.103303","intvolume":"         3","_id":"16","quality_controlled":"1","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","department":[{"_id":"BjHo"}],"citation":{"ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303."},"article_processing_charge":"No","isi":1,"title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","pubrep_id":"1062","type":"journal_article","status":"public","publication":"Physical Review Fluids","language":[{"iso":"eng"}],"year":"2018","day":"16","ec_funded":1,"file_date_updated":"2020-07-14T12:45:04Z","issue":"10","author":[{"full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","last_name":"Varshney"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"date_published":"2018-10-16T00:00:00Z","volume":3,"abstract":[{"lang":"eng","text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives."}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"date_created":"2018-12-11T11:44:10Z","article_type":"original","file":[{"date_created":"2018-12-12T10:13:56Z","creator":"system","relation":"main_file","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","file_id":"5043","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","access_level":"open_access","file_size":1838431,"date_updated":"2020-07-14T12:45:04Z","content_type":"application/pdf"}],"publisher":"American Physical Society","scopus_import":"1"},{"file":[{"file_id":"5705","date_created":"2018-12-17T12:52:12Z","creator":"dernst","checksum":"c64fff560fe5a7532ec10626ad1c215e","relation":"main_file","date_updated":"2020-07-14T12:45:04Z","content_type":"application/pdf","file_name":"2018_LNCS_Kragl.pdf","file_size":1603844,"access_level":"open_access"}],"publisher":"Springer","scopus_import":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:44:57Z","file_date_updated":"2020-07-14T12:45:04Z","date_published":"2018-07-18T00:00:00Z","abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"volume":10981,"author":[{"first_name":"Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"language":[{"iso":"eng"}],"year":"2018","day":"18","isi":1,"article_processing_charge":"No","citation":{"ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>."},"status":"public","type":"conference","title":"Layered Concurrent Programs","tmp":{"short":"CC BY (4.0)","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)"},"intvolume":"     10981","_id":"160","page":"79 - 102","external_id":{"isi":["000491481600005"]},"doi":"10.1007/978-3-319-96145-3_5","department":[{"_id":"ToHe"}],"quality_controlled":"1","alternative_title":["LNCS"],"has_accepted_license":"1","publist_id":"7761","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","month":"07","ddc":["000"],"date_updated":"2023-09-13T08:45:09Z","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, UK"},"oa":1,"publication_status":"published"},{"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"quality_controlled":"1","intvolume":"         9","_id":"161","external_id":{"isi":["000440149300021"]},"doi":"10.1038/s41467-018-05417-9","type":"journal_article","status":"public","title":"Statistical mechanics for metabolic networks during steady state growth","tmp":{"short":"CC BY (4.0)","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)"},"isi":1,"article_processing_charge":"No","citation":{"chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018."},"date_updated":"2024-02-21T13:45:39Z","ddc":["570"],"publication_status":"published","oa":1,"related_material":{"record":[{"relation":"popular_science","id":"5587","status":"public"}]},"publist_id":"7760","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","oa_version":"Published Version","article_number":"2988","has_accepted_license":"1","date_created":"2018-12-11T11:44:57Z","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"scopus_import":"1","publisher":"Springer Nature","file":[{"file_id":"5728","relation":"main_file","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","date_created":"2018-12-17T16:44:28Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:45:06Z","access_level":"open_access","file_size":1043205,"file_name":"2018_NatureComm_DeMartino.pdf"}],"ec_funded":1,"language":[{"iso":"eng"}],"year":"2018","day":"30","publication":"Nature Communications","date_published":"2018-07-30T00:00:00Z","volume":9,"abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino"},{"full_name":"Mc, Andersson Anna","first_name":"Andersson Anna","last_name":"Mc"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"issue":"1","file_date_updated":"2020-07-14T12:45:06Z"},{"tmp":{"short":"CC BY (4.0)","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)"},"title":"Social network plasticity decreases disease transmission in a eusocial insect","type":"research_data_reference","status":"public","publisher":"Zenodo","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"citation":{"ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","mla":"Stroeymeyt, Nathalie, et al. <i>Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>."},"department":[{"_id":"SyCr"}],"date_created":"2023-05-23T13:24:51Z","doi":"10.5281/ZENODO.1322669","_id":"13055","author":[{"last_name":"Stroeymeyt","first_name":"Nathalie","full_name":"Stroeymeyt, Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V"},{"last_name":"Crespi","first_name":"Alessandro","full_name":"Crespi, Alessandro"},{"full_name":"Mersch, Danielle","first_name":"Danielle","last_name":"Mersch"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Keller","full_name":"Keller, Laurent"}],"abstract":[{"lang":"eng","text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n                                                     - correction of URLs within README.txt file\r\n"}],"date_published":"2018-10-23T00:00:00Z","oa":1,"date_updated":"2023-10-17T11:50:04Z","ddc":["570"],"month":"10","oa_version":"Published Version","related_material":{"record":[{"id":"7","relation":"used_in_publication","status":"public"}]},"day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018"},{"tmp":{"short":"CC BY (4.0)","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)"},"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","status":"public","type":"research_data_reference","citation":{"ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"article_processing_charge":"No","publisher":"Zenodo","department":[{"_id":"FyKo"}],"date_created":"2023-05-23T16:08:20Z","doi":"10.5281/ZENODO.2025846","_id":"13059","author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"last_name":"di Tommaso","first_name":"Paolo","full_name":"di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"date_published":"2018-12-07T00:00:00Z","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}],"oa":1,"date_updated":"2023-09-06T14:32:51Z","ddc":["570"],"oa_version":"Published Version","month":"12","year":"2018","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"7181","relation":"used_in_publication","status":"public"}]}},{"publication_status":"published","oa":1,"date_updated":"2024-02-21T13:45:12Z","ddc":["570"],"oa_version":"Published Version","month":"08","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5586"}]},"publist_id":"7792","article_number":"e35684","has_accepted_license":"1","quality_controlled":"1","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","department":[{"_id":"BeVi"}],"external_id":{"isi":["000441388200001"]},"doi":"10.7554/eLife.35684","intvolume":"         7","_id":"131","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","tmp":{"short":"CC BY (4.0)","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)"},"status":"public","type":"journal_article","citation":{"ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>"},"article_processing_charge":"No","isi":1,"publication":"eLife","language":[{"iso":"eng"}],"year":"2018","day":"13","author":[{"full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"full_name":"Cosseau, Celine","first_name":"Celine","last_name":"Cosseau"},{"last_name":"Ferré","first_name":"Sabrina","full_name":"Ferré, Sabrina"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"full_name":"Grevelding, Christoph","first_name":"Christoph","last_name":"Grevelding"},{"full_name":"Couté, Yohann","first_name":"Yohann","last_name":"Couté"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"date_published":"2018-08-13T00:00:00Z","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"volume":7,"file_date_updated":"2020-07-14T12:44:43Z","article_type":"original","date_created":"2018-12-11T11:44:47Z","project":[{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"scopus_import":"1","publisher":"eLife Sciences Publications","file":[{"file_name":"2018_eLife_Picard.pdf","access_level":"open_access","file_size":3158125,"date_updated":"2020-07-14T12:44:43Z","content_type":"application/pdf","creator":"dernst","date_created":"2018-12-17T11:55:05Z","checksum":"d6331d4385b1fffd6b47b45d5949d841","relation":"main_file","file_id":"5695"}]},{"quality_controlled":"1","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","department":[{"_id":"EdHa"}],"external_id":{"isi":["000441327300012"]},"doi":"10.1016/j.devcel.2018.06.028","intvolume":"        46","page":"360 - 375","_id":"132","tmp":{"short":"CC BY (4.0)","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)"},"title":"Defining lineage potential and fate behavior of precursors during pancreas development","status":"public","type":"journal_article","citation":{"ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","ieee":"M. Sznurkowska <i>et al.</i>, “Defining lineage potential and fate behavior of precursors during pancreas development,” <i>Developmental Cell</i>, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. 2018;46(3):360-375. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>"},"article_processing_charge":"No","isi":1,"publication_status":"published","oa":1,"date_updated":"2023-09-11T12:52:41Z","ddc":["570"],"oa_version":"Published Version","month":"08","publist_id":"7791","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","date_created":"2018-12-11T11:44:48Z","article_type":"original","scopus_import":"1","file":[{"file_size":8948384,"access_level":"open_access","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:43Z","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","relation":"main_file","creator":"dernst","date_created":"2018-12-17T10:49:49Z","file_id":"5694"}],"publisher":"Cell Press","publication":"Developmental Cell","language":[{"iso":"eng"}],"year":"2018","day":"06","author":[{"full_name":"Sznurkowska, Magdalena","first_name":"Magdalena","last_name":"Sznurkowska"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Roberta","last_name":"Azzarelli","full_name":"Azzarelli, Roberta"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"},{"first_name":"Sonia","last_name":"Nestorowa","full_name":"Nestorowa, Sonia"},{"last_name":"Hindley","first_name":"Christopher","full_name":"Hindley, Christopher"},{"first_name":"Jennifer","last_name":"Nichols","full_name":"Nichols, Jennifer"},{"full_name":"Göttgens, Berthold","last_name":"Göttgens","first_name":"Berthold"},{"last_name":"Huch","first_name":"Meritxell","full_name":"Huch, Meritxell"},{"last_name":"Philpott","first_name":"Anna","full_name":"Philpott, Anna"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"date_published":"2018-08-06T00:00:00Z","volume":46,"abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:43Z","issue":"3"},{"issue":"36","abstract":[{"lang":"eng","text":"Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process."}],"volume":10,"date_published":"2018-08-17T00:00:00Z","author":[{"full_name":"Kretschmer, Silvan","last_name":"Kretschmer","first_name":"Silvan"},{"last_name":"Maslov","first_name":"Mikhail","orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","full_name":"Maslov, Mikhail"},{"last_name":"Ghaderzadeh","first_name":"Sadegh","full_name":"Ghaderzadeh, Sadegh"},{"last_name":"Ghorbani-Asl","first_name":"Mahdi","full_name":"Ghorbani-Asl, Mahdi"},{"full_name":"Hlawacek, Gregor","first_name":"Gregor","last_name":"Hlawacek"},{"full_name":"Krasheninnikov, Arkady V.","last_name":"Krasheninnikov","first_name":"Arkady V."}],"day":"17","year":"2018","language":[{"iso":"eng"}],"publication":"ACS Applied Materials & Interfaces","keyword":["General Materials Science"],"publisher":"American Chemical Society","pmid":1,"date_created":"2023-07-21T11:43:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"08","date_updated":"2023-08-01T07:18:30Z","publication_identifier":{"issn":["1944-8244","1944-8252"]},"publication_status":"published","article_processing_charge":"No","citation":{"chicago":"Kretschmer, Silvan, Mikhail Maslov, Sadegh Ghaderzadeh, Mahdi Ghorbani-Asl, Gregor Hlawacek, and Arkady V. Krasheninnikov. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acsami.8b08471\">https://doi.org/10.1021/acsami.8b08471</a>.","ama":"Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. <i>ACS Applied Materials &#38; Interfaces</i>. 2018;10(36):30827-30836. doi:<a href=\"https://doi.org/10.1021/acsami.8b08471\">10.1021/acsami.8b08471</a>","short":"S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, A.V. Krasheninnikov, ACS Applied Materials &#38; Interfaces 10 (2018) 30827–30836.","apa":"Kretschmer, S., Maslov, M., Ghaderzadeh, S., Ghorbani-Asl, M., Hlawacek, G., &#38; Krasheninnikov, A. V. (2018). Supported two-dimensional materials under ion irradiation: The substrate governs defect production. <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.8b08471\">https://doi.org/10.1021/acsami.8b08471</a>","mla":"Kretschmer, Silvan, et al. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 10, no. 36, American Chemical Society, 2018, pp. 30827–36, doi:<a href=\"https://doi.org/10.1021/acsami.8b08471\">10.1021/acsami.8b08471</a>.","ieee":"S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, and A. V. Krasheninnikov, “Supported two-dimensional materials under ion irradiation: The substrate governs defect production,” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 10, no. 36. American Chemical Society, pp. 30827–30836, 2018.","ista":"Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. 2018. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. ACS Applied Materials &#38; Interfaces. 10(36), 30827–30836."},"extern":"1","status":"public","type":"journal_article","title":"Supported two-dimensional materials under ion irradiation: The substrate governs defect production","page":"30827-30836","_id":"13255","intvolume":"        10","doi":"10.1021/acsami.8b08471","external_id":{"pmid":["30117320"]},"quality_controlled":"1"},{"article_number":"21","has_accepted_license":"1","alternative_title":["LIPIcs"],"publication_status":"published","oa":1,"conference":{"location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-07","name":"CONCUR: International Conference on Concurrency Theory"},"ddc":["000"],"date_updated":"2023-09-07T13:18:00Z","publication_identifier":{"issn":["18688969"]},"oa_version":"Published Version","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"6426","relation":"earlier_version"},{"id":"8332","relation":"dissertation_contains","status":"public"}]},"publist_id":"7790","tmp":{"short":"CC BY (4.0)","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)"},"title":"Synchronizing the asynchronous","status":"public","type":"conference","pubrep_id":"1039","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>","mla":"Kragl, Bernhard, et al. <i>Synchronizing the Asynchronous</i>. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>."},"quality_controlled":"1","department":[{"_id":"ToHe"}],"doi":"10.4230/LIPIcs.CONCUR.2018.21","_id":"133","intvolume":"       118","author":[{"orcid":"0000-0001-7745-9117","first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"volume":118,"abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"date_published":"2018-08-13T00:00:00Z","file_date_updated":"2020-07-14T12:44:44Z","day":"13","year":"2018","language":[{"iso":"eng"}],"scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:44Z","content_type":"application/pdf","file_name":"IST-2018-853-v2+2_concur2018.pdf","file_size":745438,"access_level":"open_access","file_id":"5368","date_created":"2018-12-12T10:18:46Z","creator":"system","checksum":"c90895f4c5fafc18ddc54d1c8848077e","relation":"main_file"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:44:48Z","project":[{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}]},{"title":"Reversible chromism of spiropyran in the cavity of a flexible coordination cage","status":"public","type":"journal_article","article_processing_charge":"No","extern":"1","citation":{"ista":"Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nature Communications. 9, 641.","ieee":"D. Samanta <i>et al.</i>, “Reversible chromism of spiropyran in the cavity of a flexible coordination cage,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","apa":"Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner, Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity of a flexible coordination cage. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-02715-6\">https://doi.org/10.1038/s41467-017-02715-6</a>","mla":"Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” <i>Nature Communications</i>, vol. 9, 641, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-017-02715-6\">10.1038/s41467-017-02715-6</a>.","ama":"Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-017-02715-6\">10.1038/s41467-017-02715-6</a>","short":"D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L. Avram, P. Král, R. Klajn, Nature Communications 9 (2018).","chicago":"Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-017-02715-6\">https://doi.org/10.1038/s41467-017-02715-6</a>."},"quality_controlled":"1","external_id":{"pmid":["29440687"]},"doi":"10.1038/s41467-017-02715-6","intvolume":"         9","_id":"13374","article_number":"641","publication_status":"published","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2023-08-07T10:54:05Z","oa_version":"Published Version","month":"02","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-018-03701-2"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-017-02715-6","open_access":"1"}],"publisher":"Springer Nature","article_type":"original","date_created":"2023-08-01T09:39:32Z","author":[{"first_name":"Dipak","last_name":"Samanta","full_name":"Samanta, Dipak"},{"first_name":"Daria","last_name":"Galaktionova","full_name":"Galaktionova, Daria"},{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"first_name":"Linda J. W.","last_name":"Shimon","full_name":"Shimon, Linda J. W."},{"full_name":"Diskin-Posner, Yael","first_name":"Yael","last_name":"Diskin-Posner"},{"first_name":"Liat","last_name":"Avram","full_name":"Avram, Liat"},{"first_name":"Petr","last_name":"Král","full_name":"Král, Petr"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"date_published":"2018-02-13T00:00:00Z","volume":9,"abstract":[{"lang":"eng","text":"Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments."}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publication":"Nature Communications","language":[{"iso":"eng"}],"year":"2018","day":"13"}]