[{"publication":"Scientific Reports","file_date_updated":"2020-07-14T12:46:02Z","pubrep_id":"1016","external_id":{"isi":["000429404300013"]},"date_created":"2018-12-11T11:45:47Z","_id":"317","month":"04","date_updated":"2023-09-13T09:38:00Z","title":"Palladium gates for reproducible quantum dots in silicon","article_processing_charge":"No","date_published":"2018-04-09T00:00:00Z","scopus_import":"1","volume":8,"intvolume":"         8","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","article_number":"5690","oa_version":"Published Version","doi":"10.1038/s41598-018-24004-y","day":"09","publisher":"Nature Publishing Group","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GeKa"}],"year":"2018","author":[{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Brauns, Matthias","last_name":"Brauns"},{"first_name":"Sergey","last_name":"Amitonov","full_name":"Amitonov, Sergey"},{"full_name":"Spruijtenburg, Paul","last_name":"Spruijtenburg","first_name":"Paul"},{"first_name":"Floris","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris"}],"isi":1,"citation":{"ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>","chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>.","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., &#38; Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018."},"type":"journal_article","file":[{"creator":"system","date_created":"2018-12-12T10:17:04Z","file_id":"5256","access_level":"open_access","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","file_size":1850530,"date_updated":"2020-07-14T12:46:02Z","content_type":"application/pdf","checksum":"20af238ca4ba6491b77270be8d826bf5","relation":"main_file"}],"ddc":["539"],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7548","abstract":[{"text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.","lang":"eng"}],"publication_status":"published","quality_controlled":"1"},{"oa":1,"intvolume":"        44","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","acknowledgement":"Short Survey","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189","open_access":"1"}],"volume":44,"scopus_import":"1","article_processing_charge":"No","date_published":"2018-02-26T00:00:00Z","month":"02","title":"A fat lot of good for wound healing","date_updated":"2023-09-08T11:42:28Z","external_id":{"isi":["000426150700002"],"pmid":["29486189"]},"date_created":"2018-12-11T11:45:47Z","_id":"318","page":"405 - 406","publication":"Developmental Cell","quality_controlled":"1","status":"public","pmid":1,"language":[{"iso":"eng"}],"publist_id":"7547","abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>.","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. <i>Developmental Cell</i>. 2018;44(4):405-406. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","apa":"Casano, A. M., &#38; Sixt, M. K. (2018). A fat lot of good for wound healing. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” <i>Developmental Cell</i>, vol. 44, no. 4. Cell Press, pp. 405–406, 2018."},"type":"journal_article","year":"2018","isi":1,"author":[{"orcid":"0000-0002-6009-6804","full_name":"Casano, Alessandra M","last_name":"Casano","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandra M"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MiSi"}],"day":"26","publisher":"Cell Press","oa_version":"Published Version","doi":"10.1016/j.devcel.2018.02.009"},{"date_created":"2018-12-11T11:44:16Z","external_id":{"isi":["000448219500005"]},"_id":"32","page":"852 - 861.e7","file_date_updated":"2020-07-14T12:46:03Z","publication":"Cell Reports","date_published":"2018-10-23T00:00:00Z","article_processing_charge":"No","month":"10","date_updated":"2023-09-11T14:13:32Z","title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","scopus_import":"1","issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","intvolume":"        25","oa":1,"volume":25,"day":"23","publisher":"Elsevier","oa_version":"Published Version","doi":"10.1016/j.celrep.2018.09.066","isi":1,"author":[{"full_name":"Chen, Ting","last_name":"Chen","first_name":"Ting"},{"first_name":"Bartosz","full_name":"Kula, Bartosz","last_name":"Kula"},{"id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","first_name":"Balint","orcid":"0000-0002-4002-4686","full_name":"Nagy, Balint","last_name":"Nagy"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"full_name":"Gall, Andrea","last_name":"Gall","first_name":"Andrea"},{"last_name":"Ehrlich","full_name":"Ehrlich, Ingrid","first_name":"Ingrid"},{"full_name":"Kukley, Maria","last_name":"Kukley","first_name":"Maria"}],"year":"2018","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"SaSi"}],"ddc":["570"],"citation":{"chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>.","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. 2018;25(4):852-861.e7. doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>.","ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7.","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., &#38; Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>","ieee":"T. Chen <i>et al.</i>, “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” <i>Cell Reports</i>, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018."},"type":"journal_article","file":[{"access_level":"open_access","file_name":"2018_CellReports_Chen.pdf","date_updated":"2020-07-14T12:46:03Z","content_type":"application/pdf","file_size":4461997,"relation":"main_file","checksum":"d9f74277fd57176e04732707d575cf08","creator":"dernst","date_created":"2018-12-17T12:42:57Z","file_id":"5703"}],"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia.","lang":"eng"}],"publication_status":"published","publist_id":"8023"},{"department":[{"_id":"PeJo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"author":[{"last_name":"Hu","full_name":"Hu, Hua","first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fabian","full_name":"Roth, Fabian","last_name":"Roth"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"year":"2018","doi":"10.1016/j.neuron.2018.02.024","oa_version":"Published Version","publisher":"Elsevier","day":"04","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. "}],"publication_status":"published","publist_id":"7545","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","quality_controlled":"1","file":[{"access_level":"open_access","file_name":"2018_Neuron_Hu.pdf","date_updated":"2020-07-14T12:46:03Z","content_type":"application/pdf","file_size":3180444,"checksum":"76070f3729f9c603e1080d0151aa2b11","relation":"main_file","creator":"dernst","date_created":"2018-12-17T10:37:50Z","file_id":"5690"}],"type":"journal_article","citation":{"apa":"Hu, H., Roth, F., Vandael, D. H., &#38; Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” <i>Neuron</i>, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. 2018;98(1):156-165. doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>.","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165."},"ddc":["570"],"title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","date_updated":"2023-09-11T12:45:10Z","month":"04","date_published":"2018-04-04T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"file_date_updated":"2020-07-14T12:46:03Z","publication":"Neuron","page":"156 - 165","_id":"320","project":[{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:48Z","external_id":{"isi":["000429192100016"]},"volume":98,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/"}]},"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        98","scopus_import":"1"},{"doi":"10.1109/TPAMI.2018.2804998","oa_version":"Published Version","publisher":"IEEE","day":"01","department":[{"_id":"ChLa"}],"author":[{"last_name":"Darrell","full_name":"Darrell, Trevor","first_name":"Trevor"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sebe","full_name":"Sebe, Nico","first_name":"Nico"},{"last_name":"Wu","full_name":"Wu, Ying","first_name":"Ying"},{"first_name":"Yan","full_name":"Yan, Yan","last_name":"Yan"}],"isi":1,"year":"2018","file":[{"file_id":"7835","creator":"dernst","date_created":"2020-05-14T12:50:48Z","relation":"main_file","checksum":"b19c75da06faf3291a3ca47dfa50ef63","file_size":141724,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:03Z","file_name":"2018_IEEE_Darrell.pdf","access_level":"open_access"}],"type":"journal_article","citation":{"mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>.","ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031.","chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>.","ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2018;40(5):1029-1031. doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., &#38; Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>"},"ddc":["000"],"article_type":"original","publication_status":"published","abstract":[{"text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems.","lang":"eng"}],"publist_id":"7544","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:03Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"1029 - 1031","_id":"321","date_created":"2018-12-11T11:45:48Z","external_id":{"isi":["000428901200001"]},"title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","date_updated":"2023-09-11T14:07:54Z","month":"05","date_published":"2018-05-01T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":40,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","intvolume":"        40","oa":1},{"intvolume":"       506","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","main_file_link":[{"url":"https://arxiv.org/abs/1412.7211","open_access":"1"}],"volume":506,"scopus_import":"1","ec_funded":1,"article_processing_charge":"No","date_published":"2018-07-15T00:00:00Z","month":"07","date_updated":"2023-09-15T12:08:38Z","title":"Quantizations of multiplicative hypertoric varieties at a root of unity","external_id":{"arxiv":["1412.7211"],"isi":["000433270600005"]},"date_created":"2018-12-11T11:45:49Z","_id":"322","project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"}],"page":"92 - 128","publication":"Journal of Algebra","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7543","abstract":[{"text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework.","lang":"eng"}],"publication_status":"published","citation":{"short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” <i>Journal of Algebra</i>, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>. World Scientific Publishing, 2018. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>.","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. 2018;506:92-128. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>."},"type":"journal_article","year":"2018","isi":1,"author":[{"last_name":"Ganev","full_name":"Ganev, Iordan V","first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"TaHa"}],"day":"15","publisher":"World Scientific Publishing","arxiv":1,"oa_version":"Preprint","doi":"10.1016/j.jalgebra.2018.03.015"},{"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"In the here presented thesis, we explore the role of branched actin networks in cell migration and antigen presentation, the two most relevant processes in dendritic cell biology. Branched actin networks construct lamellipodial protrusions at the leading edge of migrating cells. These are typically seen as adhesive structures, which mediate force transduction to the extracellular matrix that leads to forward locomotion. We ablated Arp2/3 nucleation promoting factor WAVE in DCs and found that the resulting cells lack lamellipodial protrusions. Instead, depending on the maturation state, one or multiple filopodia were formed. By challenging these cells in a variety of migration assays we found that lamellipodial protrusions are dispensable for the locomotion of leukocytes and actually dampen the speed of migration. However, lamellipodia are critically required to negotiate complex environments that DCs experience while they travel to the next draining lymph node. Taken together our results suggest that leukocyte lamellipodia have rather a sensory- than a force transducing function. Furthermore, we show for the first time structure and dynamics of dendritic cell F-actin at the immunological synapse with naïve T cells. Dendritic cell F-actin appears as dynamic foci that are nucleated by the Arp2/3 complex. WAVE ablated dendritic cells show increased membrane tension, leading to an altered ultrastructure of the immunological synapse and severe T cell priming defects. These results point towards a previously unappreciated role of the cellular mechanics of dendritic cells in T cell activation. Additionally, we present a novel cell culture based system for the differentiation of dendritic cells from conditionally immortalized hematopoietic precursors. These precursor cells are genetically tractable via the CRISPR/Cas9 system while they retain their ability to differentiate into highly migratory dendritic cells and other immune cells. This will foster the study of all aspects of dendritic cell biology and beyond. "}],"publication_status":"published","publist_id":"7542","citation":{"ama":"Leithner AF. Branched actin networks in dendritic cell biology. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>","chicago":"Leithner, Alexander F. “Branched Actin Networks in Dendritic Cell Biology.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>.","ista":"Leithner AF. 2018. Branched actin networks in dendritic cell biology. Institute of Science and Technology Austria.","mla":"Leithner, Alexander F. <i>Branched Actin Networks in Dendritic Cell Biology</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">10.15479/AT:ISTA:th_998</a>.","apa":"Leithner, A. F. (2018). <i>Branched actin networks in dendritic cell biology</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_998\">https://doi.org/10.15479/AT:ISTA:th_998</a>","short":"A.F. Leithner, Branched Actin Networks in Dendritic Cell Biology, Institute of Science and Technology Austria, 2018.","ieee":"A. F. Leithner, “Branched actin networks in dendritic cell biology,” Institute of Science and Technology Austria, 2018."},"type":"dissertation","file":[{"file_size":29027671,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-02-11T23:30:17Z","relation":"source_file","checksum":"d5e3edbac548c26c1fa43a4b37a54a4c","access_level":"closed","embargo_to":"open_access","file_name":"PhD_thesis_AlexLeithner_final_version.docx","file_id":"6219","creator":"dernst","date_created":"2019-04-05T09:23:11Z"},{"file_size":66045341,"date_updated":"2021-02-11T11:17:16Z","content_type":"application/pdf","checksum":"071f7476db29e41146824ebd0697cb10","relation":"main_file","access_level":"open_access","file_name":"PhD_thesis_AlexLeithner.pdf","file_id":"6220","creator":"dernst","embargo":"2019-04-15","date_created":"2019-04-05T09:23:11Z"}],"ddc":["571","599","610"],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"}],"year":"2018","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_998","day":"12","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"1321","status":"public","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"First of all I would like to thank Michael Sixt for giving me the opportunity to work in \r\nhis group and for his support throughout the years. He is a truly inspiring person and \r\nthe  best  boss  one  can  imagine.  I  would  also  like  to  thank  all  current  and  past \r\nmembers of the Sixt group for their help and the great working atmosphere in the lab. \r\nIt is a true privilege to work with such a bright, funny and friendly group of people and \r\nI’m  proud  that  I  could  be  part  of  it.  Furthermore,  I  would  like  to  say  ‘thank  you’  to Daria Siekhaus for all the meetings and discussion we had throughout the years \r\nand to  Federica  Benvenuti  for  being  part  of  my  committee.  I  am  also  grateful  to  Jack \r\nMerrin  in  the  nanofabrication  facility  and  all  the  people  working  in  the  bioimaging-\r\n, the electron microscopy- and the preclinical facilities.","oa":1,"month":"04","title":"Branched actin networks in dendritic cell biology","date_updated":"2023-09-07T12:39:44Z","date_published":"2018-04-12T00:00:00Z","article_processing_charge":"No","page":"99","pubrep_id":"998","file_date_updated":"2021-02-11T23:30:17Z","supervisor":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"date_created":"2018-12-11T11:45:49Z","_id":"323"},{"type":"dissertation","citation":{"apa":"Chen, C. (2018). <i>Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_997\">https://doi.org/10.15479/AT:ISTA:th_997</a>","short":"C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release, Institute of Science and Technology Austria, 2018.","ieee":"C. Chen, “Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release,” Institute of Science and Technology Austria, 2018.","chicago":"Chen, Chong. “Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_997\">https://doi.org/10.15479/AT:ISTA:th_997</a>.","ama":"Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_997\">10.15479/AT:ISTA:th_997</a>","ista":"Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria.","mla":"Chen, Chong. <i>Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_997\">10.15479/AT:ISTA:th_997</a>."},"file":[{"checksum":"8e163ae9e927401b9fa7c1b3e6a3631a","relation":"main_file","date_updated":"2020-07-14T12:46:04Z","content_type":"application/pdf","file_size":8719458,"file_name":"IST-2018-997-v1+1_Thesis_chong_a.pdf","access_level":"open_access","file_id":"5046","date_created":"2018-12-12T10:13:58Z","creator":"system"},{"relation":"source_file","checksum":"f7d7260029a5fbb5c982db61328ade52","content_type":"application/octet-stream","date_updated":"2020-07-14T12:46:04Z","file_size":47841940,"file_name":"2018_Thesis_chong_source.pages","access_level":"closed","file_id":"6221","date_created":"2019-04-05T09:25:26Z","creator":"dernst"}],"ddc":["571"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity."}],"publication_status":"published","publist_id":"7541","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_997","day":"01","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"PeJo"}],"author":[{"first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chong","last_name":"Chen"}],"year":"2018","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1117"},{"relation":"part_of_dissertation","status":"public","id":"749"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"page":"110","pubrep_id":"997","file_date_updated":"2020-07-14T12:46:04Z","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"date_created":"2018-12-11T11:45:49Z","_id":"324","month":"03","title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","date_updated":"2023-09-27T12:26:03Z","date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No"},{"day":"01","publisher":"ACM","arxiv":1,"oa_version":"Preprint","doi":"10.1145/3158122","author":[{"full_name":"Agrawal, Sheshansh","last_name":"Agrawal","first_name":"Sheshansh"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Novotny, Petr","last_name":"Novotny"}],"conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, USA","end_date":"2018-01-13","name":"POPL: Principles of Programming Languages"},"year":"2018","department":[{"_id":"KrCh"}],"citation":{"ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","apa":"Agrawal, S., Chatterjee, K., &#38; Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>","mla":"Agrawal, Sheshansh, et al. <i>Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs</i>. Vol. 2, no. POPL, 34, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>.","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>"},"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach."}],"publist_id":"7540","date_created":"2018-12-11T11:45:50Z","external_id":{"arxiv":["1709.04037"]},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"325","date_published":"2018-01-01T00:00:00Z","month":"01","date_updated":"2021-01-12T07:42:07Z","title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"POPL","oa":1,"intvolume":"         2","article_number":"34","volume":2,"main_file_link":[{"url":"https://arxiv.org/abs/1709.04037","open_access":"1"}]},{"title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","date_updated":"2023-09-19T09:58:40Z","month":"03","date_published":"2018-03-07T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:06Z","publication":"European Journal of Neuroscience","page":"1033 - 1042","_id":"326","date_created":"2018-12-11T11:45:50Z","external_id":{"isi":["000431496400001"]},"volume":47,"issue":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        47","oa":1,"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","department":[{"_id":"RySh"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"isi":1,"author":[{"last_name":"Sawada","full_name":"Sawada, Kazuaki","first_name":"Kazuaki"},{"last_name":"Kawakami","full_name":"Kawakami, Ryosuke","first_name":"Ryosuke"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tomomi","last_name":"Nemoto","full_name":"Nemoto, Tomomi"}],"year":"2018","doi":"10.1111/ejn.13901","oa_version":"Published Version","publisher":"Wiley","day":"07","abstract":[{"text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.","lang":"eng"}],"publication_status":"published","publist_id":"7539","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","quality_controlled":"1","file":[{"creator":"dernst","date_created":"2018-12-17T16:16:50Z","file_id":"5721","access_level":"open_access","file_name":"2018_EJN_Sawada.pdf","date_updated":"2020-07-14T12:46:06Z","content_type":"application/pdf","file_size":4850261,"checksum":"98e901d8229e44aa8f3b51d248dedd09","relation":"main_file"}],"citation":{"ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” <i>European Journal of Neuroscience</i>, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., &#38; Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. Wiley. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>.","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. 2018;47(9):1033-1042. doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>"},"type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"}],"ddc":["570"]},{"article_processing_charge":"No","date_published":"2018-03-19T00:00:00Z","month":"03","title":"Slow dynamics in translation-invariant quantum lattice models","date_updated":"2023-09-18T09:31:46Z","external_id":{"isi":["000427798800005"]},"date_created":"2018-12-11T11:45:50Z","_id":"327","publication":"Physical Review B","intvolume":"        97","oa":1,"issue":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","article_number":"104307","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"volume":97,"scopus_import":"1","year":"2018","author":[{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"first_name":"Marko","last_name":"Žnidarič","full_name":"Žnidarič, Marko"},{"full_name":"Medvedyeva, Mariya","last_name":"Medvedyeva","first_name":"Mariya"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"},{"first_name":"Tomaž","full_name":"Prosen, Tomaž","last_name":"Prosen"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"isi":1,"department":[{"_id":"MaSe"}],"day":"19","publisher":"American Physical Society","oa_version":"Preprint","doi":"10.1103/PhysRevB.97.104307","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7538","abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>.","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. 2018;97(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., &#38; Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” <i>Physical Review B</i>, vol. 97, no. 10. American Physical Society, 2018."},"type":"journal_article"},{"department":[{"_id":"BjHo"}],"year":"2018","author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","full_name":"Choueiri, George H"},{"last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"isi":1,"oa_version":"Preprint","doi":"10.1103/PhysRevLett.120.124501","day":"19","publisher":"American Physical Society","status":"public","language":[{"iso":"eng"}],"publist_id":"7537","publication_status":"published","abstract":[{"lang":"eng","text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society."}],"quality_controlled":"1","citation":{"ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” <i>Physical Review Letters</i>, vol. 120, no. 12. American Physical Society, 2018.","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","apa":"Choueiri, G. H., Lopez Alonso, J. M., &#38; Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>.","chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>.","ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. 2018;120(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>"},"type":"journal_article","acknowledged_ssus":[{"_id":"SSU"}],"month":"03","date_updated":"2023-10-10T13:27:44Z","title":"Exceeding the asymptotic limit of polymer drag reduction","ec_funded":1,"article_processing_charge":"No","date_published":"2018-03-19T00:00:00Z","publication":"Physical Review Letters","external_id":{"isi":["000427804000005"]},"date_created":"2018-12-11T11:45:51Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"_id":"328","main_file_link":[{"url":"https://arxiv.org/abs/1703.06271","open_access":"1"}],"volume":120,"oa":1,"intvolume":"       120","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"124501","scopus_import":"1"},{"oa_version":"Published Version","doi":"10.7717/peerj.5325","day":"01","publisher":"PeerJ","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"NiBa"}],"author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","last_name":"Ringbauer"},{"full_name":"Blum, Michaël","last_name":"Blum","first_name":"Michaël"}],"isi":1,"year":"2018","type":"journal_article","citation":{"chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. 2018;2018(10). doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","apa":"Bertl, J., Ringbauer, H., &#38; Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” <i>PeerJ</i>, vol. 2018, no. 10. PeerJ, 2018."},"file":[{"file_id":"5692","creator":"dernst","date_created":"2018-12-17T10:46:06Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","file_size":1328344,"checksum":"3334886c4b39678db4c4b74299ca14ba","relation":"main_file","access_level":"open_access","file_name":"2018_PeerJ_Bertl.pdf"}],"ddc":["576"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","pmid":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"publist_id":"8022","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:06Z","publication":"PeerJ","date_created":"2018-12-11T11:44:16Z","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"_id":"33","month":"10","date_updated":"2023-10-17T12:24:43Z","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","date_published":"2018-10-01T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":2018,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","issue":"10","intvolume":"      2018","oa":1,"article_number":"e5325"},{"type":"book","scopus_import":"1","citation":{"ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","mla":"Clarke, Edmund M., et al. <i>Handbook of Model Checking</i>. 1st ed., Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>.","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>.","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature; 2018. doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, <i>Handbook of Model Checking</i>, 1st ed. Cham: Springer Nature, 2018.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., &#38; Bloem, R. (2018). <i>Handbook of Model Checking</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools.","lang":"eng"}],"publist_id":"3340","date_created":"2018-12-11T12:02:32Z","retracted":"1","day":"08","publisher":"Springer Nature","_id":"3300","page":"XLVIII, 1212","oa_version":"None","doi":"10.1007/978-3-319-10575-8","edition":"1","date_published":"2018-06-08T00:00:00Z","author":[{"first_name":"Edmund M.","last_name":"Clarke","full_name":"Clarke, Edmund M."},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"year":"2018","article_processing_charge":"No","month":"06","title":"Handbook of Model Checking","date_updated":"2025-07-24T09:25:31Z","department":[{"_id":"ToHe"}],"publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]}},{"page":"47 - 55","_id":"34","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"date_created":"2018-12-11T11:44:16Z","title":"Sensor synthesis for POMDPs with reachability objectives","date_updated":"2023-09-19T14:44:14Z","month":"06","article_processing_charge":"No","date_published":"2018-06-01T00:00:00Z","ec_funded":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.00675"}],"volume":2018,"alternative_title":["ICAPS"],"oa":1,"intvolume":"      2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"oa_version":"Preprint","publisher":"AAAI Press","day":"01","department":[{"_id":"KrCh"}],"year":"2018","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","end_date":"2018-06-29","start_date":"2018-06-24","location":"Delft, Netherlands"},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chemlík, Martin","last_name":"Chemlík","first_name":"Martin"},{"first_name":"Ufuk","full_name":"Topcu, Ufuk","last_name":"Topcu"}],"isi":1,"citation":{"ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","mla":"Chatterjee, Krishnendu, et al. <i>Sensor Synthesis for POMDPs with Reachability Objectives</i>. Vol. 2018, AAAI Press, 2018, pp. 47–55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","apa":"Chatterjee, K., Chemlík, M., &#38; Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55."},"type":"conference","publist_id":"8021","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.07031","open_access":"1"}],"related_material":{"record":[{"id":"9293","relation":"later_version","status":"public"}]},"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"28th International Conference on Automated Planning and Scheduling ","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"_id":"35","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"date_created":"2018-12-11T11:44:17Z","title":"Algorithms and conditional lower bounds for planning problems","date_updated":"2023-09-26T10:41:41Z","month":"06","article_processing_charge":"No","date_published":"2018-06-01T00:00:00Z","ec_funded":1,"type":"conference","citation":{"ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” <i>28th International Conference on Automated Planning and Scheduling </i>, AAAI Press, 2018.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In <i>28th International Conference on Automated Planning and Scheduling </i>. AAAI Press, 2018.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: <i>28th International Conference on Automated Planning and Scheduling </i>. AAAI Press; 2018.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in <i>28th International Conference on Automated Planning and Scheduling </i>, Delft, Netherlands, 2018.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In <i>28th International Conference on Automated Planning and Scheduling </i>. Delft, Netherlands: AAAI Press."},"publist_id":"8020","publication_status":"published","abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"None","arxiv":1,"publisher":"AAAI Press","day":"01","department":[{"_id":"KrCh"}],"conference":{"location":"Delft, Netherlands","start_date":"2018-06-24","end_date":"2018-06-29","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"year":"2018","isi":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"last_name":"Svozil","full_name":"Svozil, Alexander","first_name":"Alexander"}]},{"ddc":["581"],"file":[{"file_id":"5741","creator":"dernst","date_created":"2018-12-18T09:47:51Z","file_size":3359316,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:13Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","relation":"main_file","access_level":"open_access","file_name":"2018_JournalExperimBotany_Vu.pdf"}],"citation":{"mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>.","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. 2018;69(19):4609-4624. doi:<a href=\"https://doi.org/10.1093/jxb/ery204\">10.1093/jxb/ery204</a>","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” <i>Journal of Experimental Botany</i>, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., &#38; De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery204\">https://doi.org/10.1093/jxb/ery204</a>"},"type":"journal_article","quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"publist_id":"8019","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publisher":"Oxford University Press","day":"31","doi":"10.1093/jxb/ery204","oa_version":"Published Version","author":[{"first_name":"Lam","last_name":"Vu","full_name":"Vu, Lam"},{"full_name":"Zhu, Tingting","last_name":"Zhu","first_name":"Tingting"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Brigitte","last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"isi":1,"year":"2018","department":[{"_id":"JiFr"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","issue":"19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","intvolume":"        69","oa":1,"volume":69,"_id":"36","date_created":"2018-12-11T11:44:17Z","external_id":{"isi":["000443568700010"]},"file_date_updated":"2020-07-14T12:46:13Z","publication":"Journal of Experimental Botany","page":"4609 - 4624","date_published":"2018-08-31T00:00:00Z","article_processing_charge":"No","date_updated":"2023-09-19T10:00:46Z","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","month":"08"},{"year":"2018","author":[{"last_name":"Zagórski","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"department":[{"_id":"AnKi"}],"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"publisher":"Springer Nature","series_title":"MIMB","day":"16","doi":"10.1007/978-1-4939-8772-6_4","oa_version":"Submitted Version","quality_controlled":"1","publist_id":"8018","publication_status":"published","abstract":[{"lang":"eng","text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube."}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"file":[{"content_type":"application/pdf","date_updated":"2020-10-13T14:20:37Z","file_size":4906815,"checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","relation":"main_file","success":1,"access_level":"open_access","file_name":"2018_MIMB_Zagorski.pdf","file_id":"8656","date_created":"2020-10-13T14:20:37Z","creator":"dernst"}],"citation":{"ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: <i>Morphogen Gradients </i>. Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In <i>Morphogen Gradients </i>, 1863:47–63. MIMB. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">10.1007/978-1-4939-8772-6_4</a>.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","apa":"Zagórski, M. P., &#38; Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In <i>Morphogen Gradients </i> (Vol. 1863, pp. 47–63). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-8772-6_4\">https://doi.org/10.1007/978-1-4939-8772-6_4</a>","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in <i>Morphogen Gradients </i>, vol. 1863, Springer Nature, 2018, pp. 47–63."},"type":"book_chapter","article_processing_charge":"No","date_published":"2018-10-16T00:00:00Z","ec_funded":1,"date_updated":"2021-01-12T07:49:03Z","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","month":"10","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"_id":"37","date_created":"2018-12-11T11:44:17Z","publication":"Morphogen Gradients ","file_date_updated":"2020-10-13T14:20:37Z","page":"47 - 63","intvolume":"      1863","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":1863,"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1"},{"publication":"PNAS","file_date_updated":"2020-07-14T12:46:16Z","page":"11006 - 11011","_id":"38","external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","title":"Selection and gene flow shape genomic islands that control floral guides","month":"10","article_processing_charge":"No","date_published":"2018-10-23T00:00:00Z","scopus_import":"1","volume":115,"oa":1,"intvolume":"       115","issue":"43","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":" ERC Grant 201252 (to N.H.B.)","doi":"10.1073/pnas.1801832115","oa_version":"Published Version","publisher":"National Academy of Sciences","day":"23","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["00278424"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2018","isi":1,"author":[{"last_name":"Tavares","full_name":"Tavares, Hugo","first_name":"Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Desmond","last_name":"Bradley","full_name":"Bradley, Desmond"},{"first_name":"Matthew","full_name":"Couchman, Matthew","last_name":"Couchman"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"last_name":"Elleouet","full_name":"Elleouet, Joane","first_name":"Joane"},{"first_name":"Monique","full_name":"Burrus, Monique","last_name":"Burrus"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"last_name":"Li","full_name":"Li, Miaomiao","first_name":"Miaomiao"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"last_name":"Xue","full_name":"Xue, Yongbiao","first_name":"Yongbiao"},{"first_name":"Alexandra B","full_name":"Rebocho, Alexandra B","last_name":"Rebocho"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"file":[{"creator":"dernst","date_created":"2018-12-17T08:44:03Z","file_id":"5683","file_name":"11006.full.pdf","access_level":"open_access","relation":"main_file","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","file_size":1911302}],"citation":{"ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. 2018;115(43):11006-11011. doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>","ieee":"H. Tavares <i>et al.</i>, “Selection and gene flow shape genomic islands that control floral guides,” <i>PNAS</i>, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>"},"type":"journal_article","ddc":["570"],"publist_id":"8017","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"publication_status":"published","pmid":1,"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1"},{"ddc":["576"],"file":[{"access_level":"open_access","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","file_size":691602,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","relation":"main_file","checksum":"458a7c2c2e79528567edfeb0f326cbe0","creator":"system","date_created":"2018-12-12T10:08:07Z","file_id":"4667"}],"citation":{"ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., &#38; Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. 2018;10(3):928-938. doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>"},"type":"journal_article","quality_controlled":"1","publist_id":"7445","abstract":[{"text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publisher":"Oxford University Press","day":"01","doi":"10.1093/gbe/evy049","oa_version":"Published Version","year":"2018","isi":1,"author":[{"full_name":"Hönigschmid, Peter","last_name":"Hönigschmid","first_name":"Peter"},{"first_name":"Nadya","full_name":"Bykova, Nadya","last_name":"Bykova"},{"first_name":"René","full_name":"Schneider, René","last_name":"Schneider"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"first_name":"Dmitrij","full_name":"Frishman, Dmitrij","last_name":"Frishman"}],"department":[{"_id":"FyKo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","intvolume":"        10","oa":1,"issue":"3","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft  (grant  number  FR  1411/9-1).  This work  was  supported  by  the  German  Research  Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10,"_id":"384","external_id":{"isi":["000429483700022"]},"date_created":"2018-12-11T11:46:10Z","publication":"Genome Biology and Evolution","file_date_updated":"2020-07-14T12:46:16Z","pubrep_id":"999","page":"928 - 938","article_processing_charge":"No","date_published":"2018-03-01T00:00:00Z","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","date_updated":"2023-09-11T13:56:52Z","month":"03"}]