[{"month":"06","doi":"10.1016/j.phytochem.2018.02.015","language":[{"iso":"eng"}],"external_id":{"isi":["000435623400001"]},"quality_controlled":"1","isi":1,"publist_id":"7422","author":[{"full_name":"Kubiasová, Karolina","last_name":"Kubiasová","first_name":"Karolina"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"last_name":"Nisler","first_name":"Jaroslav","full_name":"Nisler, Jaroslav"},{"full_name":"Hönig, Martin","last_name":"Hönig","first_name":"Martin"},{"full_name":"Husičková, Alexandra","last_name":"Husičková","first_name":"Alexandra"},{"last_name":"Spíchal","first_name":"Lukáš","full_name":"Spíchal, Lukáš"},{"last_name":"Pěkná","first_name":"Zuzana","full_name":"Pěkná, Zuzana"},{"full_name":"Šamajová, Olga","last_name":"Šamajová","first_name":"Olga"},{"full_name":"Doležal, Karel","first_name":"Karel","last_name":"Doležal"},{"first_name":"Ondřej","last_name":"Plíhal","full_name":"Plíhal, Ondřej"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"full_name":"Plíhalová, Lucie","first_name":"Lucie","last_name":"Plíhalová"}],"volume":150,"date_created":"2018-12-11T11:46:18Z","date_updated":"2023-09-11T12:53:11Z","year":"2018","acknowledgement":"This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n","publisher":"Elsevier","department":[{"_id":"EvBe"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","citation":{"short":"K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11.","mla":"Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015.","chicago":"Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015.","ama":"Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015","ieee":"K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018.","apa":"Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015","ista":"Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11."},"publication":"Phytochemistry","page":"1-11","abstract":[{"text":"Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy.","lang":"eng"}],"type":"journal_article","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"407","intvolume":" 150","status":"public","title":"Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins"},{"date_published":"2018-10-15T00:00:00Z","citation":{"chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122.","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018.","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122"},"publication":"Physical Review B","article_type":"original","article_processing_charge":"No","day":"15","scopus_import":"1","oa_version":"Preprint","_id":"46","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 98","title":"Detection and characterization of many-body localization in central spin models","status":"public","issue":"16","abstract":[{"lang":"eng","text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase."}],"type":"journal_article","doi":"10.1103/PhysRevB.98.161122","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.08316"}],"external_id":{"isi":["000448596500002"],"arxiv":["1806.08316"]},"quality_controlled":"1","isi":1,"month":"10","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"full_name":"Yao, Norman","first_name":"Norman","last_name":"Yao"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"last_name":"Pollmann","first_name":"Frank","full_name":"Pollmann, Frank"},{"first_name":"Björn","last_name":"Trauzettel","full_name":"Trauzettel, Björn"}],"volume":98,"date_created":"2018-12-11T11:44:20Z","date_updated":"2023-09-11T12:55:03Z","acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","year":"2018","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","publist_id":"8008","article_number":"161122"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"308","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","status":"public","intvolume":" 45","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"issue":"3","publication":"Developmental Cell","citation":{"chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346.","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002"},"article_type":"original","page":"331 - 346","date_published":"2018-05-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"publisher":"Elsevier","author":[{"last_name":"Ratheesh","first_name":"Aparna","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","full_name":"Ratheesh, Aparna"},{"full_name":"Biebl, Julia","first_name":"Julia","last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Smutny","first_name":"Michael","full_name":"Smutny, Michael"},{"full_name":"Veselá, Jana","last_name":"Veselá","first_name":"Jana","id":"433253EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"György, Attila","last_name":"György","first_name":"Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6009-6804","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","last_name":"Casano","first_name":"Alessandra M","full_name":"Casano, Alessandra M"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2018-12-11T11:45:44Z","date_updated":"2023-09-11T13:22:13Z","volume":45,"ec_funded":1,"external_id":{"pmid":["29738712"],"isi":["000432461400009"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.04.002","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.devcel.2018.04.002","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"month":"05"},{"issue":"10","abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"type":"journal_article","pubrep_id":"1061","file":[{"content_type":"application/pdf","file_size":1409040,"creator":"system","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:12Z","date_created":"2018-12-12T10:10:14Z","checksum":"e1445be33e8165114e96246275600750","relation":"main_file","file_id":"4800"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"17","intvolume":" 3","status":"public","ddc":["532"],"title":"Drag enhancement and drag reduction in viscoelastic flow","article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2018-10-15T00:00:00Z","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302."},"publication":"Physical Review Fluids","ec_funded":1,"publist_id":"8038","file_date_updated":"2020-07-14T12:45:12Z","article_number":"103302 ","author":[{"orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"volume":3,"date_created":"2018-12-11T11:44:11Z","date_updated":"2023-09-11T12:59:28Z","year":"2018","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","month":"10","doi":"10.1103/PhysRevFluids.3.103302","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000447311500001"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1},{"doi":"10.1073/pnas.1716659115","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"external_id":{"isi":["000434114900071"],"pmid":["29784812"]},"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"isi":1,"quality_controlled":"1","month":"06","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Granados, Alejandro","last_name":"Granados","first_name":"Alejandro"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"last_name":"Farquhar","first_name":"Isebail","full_name":"Farquhar, Isebail"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"first_name":"Peter","last_name":"Swain","full_name":"Swain, Peter"}],"volume":115,"date_created":"2018-12-11T11:45:35Z","date_updated":"2023-09-11T12:58:24Z","pmid":1,"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","year":"2018","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","publist_id":"7618","date_published":"2018-06-05T00:00:00Z","citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115"},"publication":"PNAS","page":"6088 - 6093","article_type":"original","article_processing_charge":"No","day":"05","scopus_import":"1","oa_version":"Preprint","_id":"281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 115","status":"public","title":"Distributed and dynamic intracellular organization of extracellular information","issue":"23","abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"type":"journal_article"},{"intvolume":" 131","status":"public","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","_id":"620","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"citation":{"ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696."},"publication":"Journal of Cell Science","date_published":"2018-01-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04","publisher":"Company of Biologists","department":[{"_id":"DaSi"}],"publication_status":"published","pmid":1,"year":"2018","volume":131,"date_updated":"2023-09-11T12:57:13Z","date_created":"2018-12-11T11:47:32Z","author":[{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"last_name":"Wada","first_name":"Suguru","full_name":"Wada, Suguru"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"article_number":"jcs207696","publist_id":"7184","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.207696","month":"01"},{"abstract":[{"text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.","lang":"eng"}],"alternative_title":["HSCC Proceedings"],"type":"conference","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7833","checksum":"81eabc96430e84336ea88310ac0a1ad0","date_updated":"2020-07-14T12:45:17Z","date_created":"2020-05-14T12:18:29Z","access_level":"open_access","file_name":"2018_HSCC_Bakhirkin.pdf","content_type":"application/pdf","file_size":5900421,"creator":"dernst"}],"status":"public","ddc":["000"],"title":"Efficient parametric identification for STL","_id":"182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-04-11T00:00:00Z","page":"177 - 186","citation":{"ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132."},"publication":"Proceedings of the 21st International Conference on Hybrid Systems","publist_id":"7739","file_date_updated":"2020-07-14T12:45:17Z","date_updated":"2023-09-11T13:30:51Z","date_created":"2018-12-11T11:45:04Z","author":[{"full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin","first_name":"Alexey"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"}],"department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","year":"2018","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1145/3178126.3178132","conference":{"location":"Porto, Portugal","start_date":"2018-04-11","end_date":"2018-04-13","name":"HSCC: Hybrid Systems: Computation and Control"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000474781600020"]},"oa":1},{"date_published":"2018-07-09T00:00:00Z","page":"185 - 194","citation":{"ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194."},"article_processing_charge":"No","day":"09","scopus_import":"1","oa_version":"Preprint","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","status":"public","_id":"143","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis."}],"alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1145/3209108.3209191","conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-09","end_date":"2018-07-12","name":"LICS: Logic in Computer Science"},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000545262800020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"publication_identifier":{"isbn":["978-1-4503-5583-4"]},"month":"07","volume":"F138033","date_created":"2018-12-11T11:44:51Z","date_updated":"2023-09-11T13:23:42Z","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kučera, Antonín","first_name":"Antonín","last_name":"Kučera"},{"full_name":"Novotny, Petr","first_name":"Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik","last_name":"Velan","full_name":"Velan, Dominik"},{"first_name":"Florian","last_name":"Zuleger","full_name":"Zuleger, Florian"}],"publisher":"IEEE","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","publist_id":"7780","ec_funded":1},{"day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-28T00:00:00Z","page":"3693-3701","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","citation":{"mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389"},"abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"type":"conference","oa_version":"Preprint","status":"public","title":"Efficient optimization for rank-based loss functions","_id":"273","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","publication_identifier":{"isbn":["9781538664209"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-22","start_date":"2018-06-18","location":"Salt Lake City, UT, USA","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"doi":"10.1109/cvpr.2018.00389","isi":1,"quality_controlled":"1","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"ec_funded":1,"date_updated":"2023-09-11T13:24:43Z","date_created":"2018-12-11T11:45:33Z","author":[{"full_name":"Mohapatra, Pritish","last_name":"Mohapatra","first_name":"Pritish"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"last_name":"Jawahar","first_name":"C V","full_name":"Jawahar, C V"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Kumar, M Pawan","last_name":"Kumar","first_name":"M Pawan"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"VlKo"}],"year":"2018"},{"article_type":"original","citation":{"chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601"},"publication":"Physical Review Letters","date_published":"2018-10-19T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"19","intvolume":" 121","status":"public","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","_id":"289","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry."}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.121.167601","month":"10","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","year":"2018","volume":121,"date_updated":"2023-09-11T13:39:50Z","date_created":"2018-12-11T11:45:38Z","author":[{"full_name":"Zibrov, Alexander","last_name":"Zibrov","first_name":"Alexander"},{"orcid":"0000-0003-1250-0021","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","last_name":"Peng","first_name":"Rao","full_name":"Peng, Rao"},{"full_name":"Kometter, Carlos","last_name":"Kometter","first_name":"Carlos"},{"full_name":"Li, Jia","last_name":"Li","first_name":"Jia"},{"full_name":"Dean, Cory","first_name":"Cory","last_name":"Dean"},{"full_name":"Taniguchi, Takashi","last_name":"Taniguchi","first_name":"Takashi"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Young, Andrea","first_name":"Andrea","last_name":"Young"}],"article_number":"167601"},{"ec_funded":1,"publication_status":"published","publisher":"Frontiers in Bioscience","department":[{"_id":"JoFi"}],"year":"2018","acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","pmid":1,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-11T13:38:14Z","volume":23,"author":[{"last_name":"Salari","first_name":"Vahid","full_name":"Salari, Vahid"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"full_name":"Simon, Christoph","first_name":"Christoph","last_name":"Simon"},{"full_name":"Scholkmann, Felix","last_name":"Scholkmann","first_name":"Felix"},{"first_name":"Zahra","last_name":"Alirezaei","full_name":"Alirezaei, Zahra"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"}],"month":"03","quality_controlled":"1","isi":1,"project":[{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"external_id":{"isi":["000439042800001"],"pmid":["29293441"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"language":[{"iso":"eng"}],"doi":"10.2741/4651","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"issue":"8","title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","status":"public","intvolume":" 23","_id":"287","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","page":"1391 - 1406","publication":"Frontiers in Bioscience - Landmark","citation":{"chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651"},"date_published":"2018-03-01T00:00:00Z"},{"status":"public","title":"Embeddability in the 3-Sphere is decidable","intvolume":" 65","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"425","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"issue":"1","article_type":"original","publication":"Journal of the ACM","citation":{"short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5."},"date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"year":"2018","date_created":"2018-12-11T11:46:24Z","date_updated":"2023-09-11T13:38:49Z","volume":65,"author":[{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2157"}]},"article_number":"5","ec_funded":1,"publist_id":"7398","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"language":[{"iso":"eng"}],"doi":"10.1145/3078632","month":"01"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:09Z","ec_funded":1,"publist_id":"7250","date_updated":"2023-09-11T13:41:22Z","date_created":"2018-12-11T11:47:12Z","volume":122,"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.11.007","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000440392900014"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"issue":"7","type":"journal_article","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7199","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_name":"bartonetheridge.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2287682,"creator":"nbarton"}],"title":"Establishment in a new habitat by polygenic adaptation","status":"public","ddc":["519","576"],"intvolume":" 122","_id":"564","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"110-127","publication":"Theoretical Population Biology","citation":{"ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007."}},{"type":"journal_article","issue":"7713","abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"intvolume":" 559","title":"Evolution of cooperation in stochastic games","ddc":["000"],"status":"public","_id":"157","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2018_Nature_Hilbe.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2834442,"creator":"dernst","relation":"main_file","file_id":"7049","date_updated":"2020-07-14T12:45:02Z","date_created":"2019-11-19T08:09:57Z","checksum":"011ab905cf9a410bc2b96f15174d654d"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","page":"246 - 249","citation":{"chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x"},"publication":"Nature","date_published":"2018-07-04T00:00:00Z","ec_funded":1,"publist_id":"7764","file_date_updated":"2020-07-14T12:45:02Z","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2018","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","volume":559,"date_created":"2018-12-11T11:44:56Z","date_updated":"2023-09-11T13:43:22Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"full_name":"Šimsa, Štepán","first_name":"Štepán","last_name":"Šimsa"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"month":"07","project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000438240900054"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41586-018-0277-x"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"3","status":"public","ddc":["576"],"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"384","oa_version":"Published Version","file":[{"file_id":"4667","relation":"main_file","checksum":"458a7c2c2e79528567edfeb0f326cbe0","date_created":"2018-12-12T10:08:07Z","date_updated":"2020-07-14T12:46:16Z","access_level":"open_access","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","creator":"system","file_size":691602,"content_type":"application/pdf"}],"pubrep_id":"999","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"928 - 938","publication":"Genome Biology and Evolution","citation":{"ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","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.","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,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","apa":"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. Oxford University Press. https://doi.org/10.1093/gbe/evy049","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","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.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049."},"date_published":"2018-03-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"7445","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"FyKo"}],"year":"2018","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","date_created":"2018-12-11T11:46:10Z","date_updated":"2023-09-11T13:56:52Z","volume":10,"author":[{"full_name":"Hönigschmid, Peter","last_name":"Hönigschmid","first_name":"Peter"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"first_name":"René","last_name":"Schneider","full_name":"Schneider, René"},{"full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitrij","last_name":"Frishman","full_name":"Frishman, Dmitrij"}],"month":"03","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000429483700022"]},"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evy049"},{"month":"03","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300638","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"oa":1,"external_id":{"isi":["000426219600025"]},"publist_id":"7251","volume":208,"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:42:38Z","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald"},{"last_name":"Kolesnikov","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander"},{"last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publication_status":"published","year":"2018","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","page":"1231-1245","citation":{"ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638."},"publication":"Genetics","issue":"3","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 208","status":"public","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"563"},{"date_published":"2018-05-22T00:00:00Z","publication":"Computer Graphics Forum","citation":{"ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177."},"article_type":"original","page":"169 - 177","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_created":"2020-10-08T08:38:23Z","date_updated":"2020-10-08T08:38:23Z","success":1,"checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627","relation":"main_file","creator":"wojtan","content_type":"application/pdf","file_size":54309947,"file_name":"exnbflip.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"135","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["006"],"title":"Extended narrow band FLIP for liquid simulations","intvolume":" 37","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"issue":"2","type":"journal_article","alternative_title":["Eurographics"],"doi":"10.1111/cgf.13351","language":[{"iso":"eng"}],"external_id":{"isi":["000434085600016"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"month":"05","publication_identifier":{"issn":["0167-7055"]},"author":[{"full_name":"Sato, Takahiro","first_name":"Takahiro","last_name":"Sato"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"}],"date_created":"2018-12-11T11:44:49Z","date_updated":"2023-09-11T14:00:26Z","volume":37,"year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:38:23Z","ec_funded":1},{"abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","status":"public","intvolume":" 209","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"316","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"861-883","publication":"Genetics","citation":{"chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748"},"ec_funded":1,"date_updated":"2023-09-11T13:57:43Z","date_created":"2018-12-11T11:45:47Z","volume":209,"author":[{"full_name":"Bodova, Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova"},{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"}],"related_material":{"record":[{"id":"9813","status":"public","relation":"research_data"}],"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"isi":["000437171700017"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"oa":1},{"month":"07","doi":"10.1002/jez.b.22824","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["29998472"],"isi":["000443231000002"]},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"quality_controlled":"1","isi":1,"publist_id":"7730","author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"full_name":"Kremer, Lucas","last_name":"Kremer","first_name":"Lucas"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"},{"full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"full_name":"Puilachs, Maria","first_name":"Maria","last_name":"Puilachs"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"}],"volume":330,"date_updated":"2023-09-11T13:59:54Z","date_created":"2018-12-11T11:45:06Z","pmid":1,"year":"2018","publisher":"Wiley","department":[{"_id":"BeVi"}],"publication_status":"published","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2018-07-11T00:00:00Z","citation":{"ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley. https://doi.org/10.1002/jez.b.22824","ieee":"M. Harrison et al., “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330. Wiley, pp. 254–264, 2018.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824."},"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","page":"254-264","article_type":"original","abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"type":"journal_article","oa_version":"Submitted Version","_id":"190","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 330","status":"public","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"404","intvolume":" 50","ddc":["510"],"status":"public","title":"Existence of positive solutions to stochastic thin-film equations","file":[{"checksum":"89a8eae7c52bb356c04f52b44bff4b5a","date_created":"2019-11-07T12:20:25Z","date_updated":"2020-07-14T12:46:22Z","file_id":"6992","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":557338,"access_level":"open_access","file_name":"2018_SIAM_Fischer.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n"}],"citation":{"chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796"},"publication":"SIAM Journal on Mathematical Analysis","page":"411 - 455","article_type":"original","date_published":"2018-01-30T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","year":"2018","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"JuFi"}],"publication_status":"published","author":[{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"},{"first_name":"Günther","last_name":"Grün","full_name":"Grün, Günther"}],"volume":50,"date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-11T13:59:22Z","publist_id":"7425","file_date_updated":"2020-07-14T12:46:22Z","oa":1,"external_id":{"isi":["000426630900015"]},"isi":1,"quality_controlled":"1","doi":"10.1137/16M1098796","language":[{"iso":"eng"}],"month":"01"},{"type":"research_data_reference","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"year":"2018","_id":"9813","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","status":"public","title":"Supplemental material for Bodova et al., 2018","related_material":{"record":[{"id":"316","relation":"used_in_publication","status":"public"}]},"author":[{"orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","first_name":"Katarína","full_name":"Bod'ová, Katarína"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas","full_name":"Priklopil, Tadeas"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_updated":"2023-09-11T13:57:42Z","date_created":"2021-08-06T13:04:32Z","article_processing_charge":"No","day":"30","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"citation":{"ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1."},"oa":1,"date_published":"2018-04-30T00:00:00Z","doi":"10.25386/genetics.6148304.v1"},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732."},"page":"12728-12732","date_published":"2018-12-11T00:00:00Z","scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5780","ddc":["580"],"title":"Genetically encodable bioluminescent system from fungi","status":"public","intvolume":" 115","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_PNAS_Kotlobay.pdf","file_size":1271988,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5926","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","date_created":"2019-02-05T15:21:40Z","date_updated":"2020-07-14T12:47:11Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"issue":"50","external_id":{"isi":["000452866000068"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.1803615115","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["00278424"]},"year":"2018","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"FyKo"}],"author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","first_name":"Karen","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen"},{"full_name":"Mokrushina, Yuliana A.","first_name":"Yuliana A.","last_name":"Mokrushina"},{"last_name":"Marcet-Houben","first_name":"Marina","full_name":"Marcet-Houben, Marina"},{"full_name":"Serebrovskaya, Ekaterina O.","first_name":"Ekaterina O.","last_name":"Serebrovskaya"},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa"},{"first_name":"Andrey Y.","last_name":"Gorokhovatsky","full_name":"Gorokhovatsky, Andrey Y."},{"first_name":"Andrey","last_name":"Vvedensky","full_name":"Vvedensky, Andrey"},{"first_name":"Konstantin V.","last_name":"Purtov","full_name":"Purtov, Konstantin V."},{"first_name":"Valentin N.","last_name":"Petushkov","full_name":"Petushkov, Valentin N."},{"first_name":"Natalja S.","last_name":"Rodionova","full_name":"Rodionova, Natalja S."},{"first_name":"Tatiana V.","last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V."},{"full_name":"Fakhranurova, Liliia","first_name":"Liliia","last_name":"Fakhranurova"},{"full_name":"Guglya, Elena B.","first_name":"Elena B.","last_name":"Guglya"},{"first_name":"Rustam","last_name":"Ziganshin","full_name":"Ziganshin, Rustam"},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"first_name":"Zinaida M.","last_name":"Kaskova","full_name":"Kaskova, Zinaida M."},{"last_name":"Shender","first_name":"Victoria","full_name":"Shender, Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"last_name":"Abakumova","first_name":"Tatiana O.","full_name":"Abakumova, Tatiana O."},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Eroshkin, Fedor M.","last_name":"Eroshkin","first_name":"Fedor M."},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"full_name":"Kopantzev, Eugene P.","last_name":"Kopantzev","first_name":"Eugene P."},{"last_name":"Waldenmaier","first_name":"Hans E.","full_name":"Waldenmaier, Hans E."},{"first_name":"Anderson G.","last_name":"Oliveira","full_name":"Oliveira, Anderson G."},{"first_name":"Yuichi","last_name":"Oba","full_name":"Oba, Yuichi"},{"last_name":"Barsova","first_name":"Ekaterina","full_name":"Barsova, Ekaterina"},{"last_name":"Bogdanova","first_name":"Ekaterina A.","full_name":"Bogdanova, Ekaterina A."},{"full_name":"Gabaldón, Toni","first_name":"Toni","last_name":"Gabaldón"},{"last_name":"Stevani","first_name":"Cassius V.","full_name":"Stevani, Cassius V."},{"full_name":"Lukyanov, Sergey","last_name":"Lukyanov","first_name":"Sergey"},{"first_name":"Ivan V.","last_name":"Smirnov","full_name":"Smirnov, Ivan V."},{"full_name":"Gitelson, Josef I.","first_name":"Josef I.","last_name":"Gitelson"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."}],"date_created":"2018-12-23T22:59:18Z","date_updated":"2023-09-11T14:04:05Z","volume":115,"file_date_updated":"2020-07-14T12:47:11Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"428","intvolume":" 115","status":"public","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","ddc":["580"],"oa_version":"Published Version","file":[{"file_id":"5700","relation":"main_file","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","date_created":"2018-12-17T12:30:14Z","date_updated":"2020-07-14T12:46:26Z","access_level":"open_access","file_name":"2018_PNAS_Salanenka.pdf","creator":"dernst","content_type":"application/pdf","file_size":1924101}],"type":"journal_article","issue":"14","abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"citation":{"mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115"},"publication":"PNAS","page":" 3716 - 3721","date_published":"2018-04-03T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","year":"2018","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"first_name":"Yuliya","last_name":"Salanenka","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya"},{"full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"full_name":"Löfke, Christian","first_name":"Christian","last_name":"Löfke"},{"full_name":"Tabata, Kaori","last_name":"Tabata","first_name":"Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"volume":115,"date_created":"2018-12-11T11:46:25Z","date_updated":"2023-09-11T14:06:34Z","ec_funded":1,"publist_id":"7395","file_date_updated":"2020-07-14T12:46:26Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000429012500073"]},"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.1721760115","language":[{"iso":"eng"}],"month":"04"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"issue":"1","ddc":["570"],"title":"Flexible learning-free segmentation and reconstruction of neural volumes","status":"public","intvolume":" 8","_id":"62","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"2018_ScientificReports_Shahbazi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4141645,"file_id":"5699","relation":"main_file","date_updated":"2020-07-14T12:47:24Z","date_created":"2018-12-17T12:22:24Z","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2"}],"scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Scientific Reports","citation":{"mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3"},"date_published":"2018-09-24T00:00:00Z","article_number":"14247","file_date_updated":"2020-07-14T12:47:24Z","publist_id":"7992","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","year":"2018","date_created":"2018-12-11T11:44:25Z","date_updated":"2023-09-11T14:02:55Z","volume":8,"author":[{"full_name":"Shabazi, Ali","last_name":"Shabazi","first_name":"Ali"},{"last_name":"Kinnison","first_name":"Jeffery","full_name":"Kinnison, Jeffery"},{"first_name":"Rafael","last_name":"Vescovi","full_name":"Vescovi, Rafael"},{"first_name":"Ming","last_name":"Du","full_name":"Du, Ming"},{"last_name":"Hill","first_name":"Robert","full_name":"Hill, Robert"},{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"},{"full_name":"Takeno, Marc","first_name":"Marc","last_name":"Takeno"},{"full_name":"Zeng, Hongkui","last_name":"Zeng","first_name":"Hongkui"},{"last_name":"Da Costa","first_name":"Nuno","full_name":"Da Costa, Nuno"},{"full_name":"Grutzendler, Jaime","last_name":"Grutzendler","first_name":"Jaime"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"last_name":"Scheirer","first_name":"Walter","full_name":"Scheirer, Walter"}],"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"month":"09","isi":1,"quality_controlled":"1","external_id":{"isi":["000445336600015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-32628-3"},{"quality_controlled":"1","isi":1,"project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000434963700016"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1002/eji.201747358","month":"02","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Wiley-Blackwell","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","year":"2018","date_created":"2018-12-11T11:46:28Z","date_updated":"2023-09-11T14:01:18Z","volume":48,"author":[{"full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"},{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Haecker, Hans","first_name":"Hans","last_name":"Haecker"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"file_date_updated":"2020-07-14T12:46:27Z","ec_funded":1,"publist_id":"7386","page":"1074 - 1077","publication":"European Journal of Immunology","citation":{"short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077."},"date_published":"2018-02-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","ddc":["570"],"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","status":"public","intvolume":" 48","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"437","file":[{"content_type":"application/pdf","file_size":590106,"creator":"system","access_level":"open_access","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:46:27Z","relation":"main_file","file_id":"5044"}],"oa_version":"Published Version","pubrep_id":"1067","type":"journal_article","abstract":[{"text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.","lang":"eng"}],"issue":"6"},{"date_published":"2018-01-01T00:00:00Z","article_type":"original","page":"159 - 171","publication":"Journal of Evolutionary Biology","citation":{"short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211","ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","intvolume":" 31","_id":"617","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/jeb.13211","quality_controlled":"1","isi":1,"external_id":{"isi":["000419307000014"],"pmid":["29150962"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"oa":1,"month":"01","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"date_updated":"2023-09-11T14:06:04Z","date_created":"2018-12-11T11:47:31Z","volume":31,"author":[{"full_name":"Kutzer, Megan","first_name":"Megan","last_name":"Kutzer","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"full_name":"Armitage, Sophie","last_name":"Armitage","first_name":"Sophie"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"SyCr"}],"acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","year":"2018","pmid":1,"publist_id":"7187"},{"author":[{"first_name":"Dora-Clara","last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"volume":50,"date_created":"2019-01-27T22:59:11Z","date_updated":"2023-09-11T14:04:41Z","pmid":1,"year":"2018","department":[{"_id":"GaNo"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2020-07-14T12:47:13Z","article_number":"100","doi":"10.1038/s12276-018-0129-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2092-6413"]},"month":"08","file":[{"date_updated":"2020-07-14T12:47:13Z","date_created":"2019-01-28T15:18:02Z","checksum":"4498301c8c53097c9a1a8ef990936eb5","relation":"main_file","file_id":"5893","file_size":1237482,"content_type":"application/pdf","creator":"dernst","file_name":"2018_EMM_Tarlungeanu.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5888","intvolume":" 50","status":"public","ddc":["570"],"title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","issue":"8","abstract":[{"text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice.","lang":"eng"}],"type":"journal_article","date_published":"2018-08-07T00:00:00Z","citation":{"chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018).","ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7"},"publication":"Experimental & Molecular Medicine","has_accepted_license":"1","article_processing_charge":"No","day":"07","scopus_import":"1"},{"doi":"10.1007/s11005-018-1091-y","language":[{"iso":"eng"}],"external_id":{"isi":["000446491500008"],"arxiv":["1712.06218"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","month":"05","author":[{"first_name":"Douglas","last_name":"Lundholm","full_name":"Lundholm, Douglas"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"volume":108,"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-11T14:01:57Z","acknowledgement":"Financial support from the Swedish Research Council, grant no. 2013-4734 (D. L.), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 694227, R. S.), and by the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully acknowledged.","year":"2018","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"publist_id":"7586","file_date_updated":"2020-07-14T12:45:55Z","date_published":"2018-05-11T00:00:00Z","citation":{"ista":"Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 108(11), 2523–2541.","ieee":"D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.","apa":"Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y","ama":"Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y","chicago":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.","mla":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp. 2523–41, doi:10.1007/s11005-018-1091-y.","short":"D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541."},"publication":"Letters in Mathematical Physics","page":"2523-2541","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"5698","relation":"main_file","checksum":"8beb9632fa41bbd19452f55f31286a31","date_created":"2018-12-17T12:14:17Z","date_updated":"2020-07-14T12:45:55Z","access_level":"open_access","file_name":"2018_LettMathPhys_Lundholm.pdf","creator":"dernst","content_type":"application/pdf","file_size":551996}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"295","intvolume":" 108","title":"Fermionic behavior of ideal anyons","ddc":["510"],"status":"public","issue":"11","abstract":[{"lang":"eng","text":"We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons."}],"type":"journal_article"},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"65 - 74","publication":"Current Opinion in Structural Biology","citation":{"mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018, pp. 65–74, doi:10.1016/j.sbi.2017.12.002.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 2018;50:65-74. doi:10.1016/j.sbi.2017.12.002","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” Current Opinion in Structural Biology, vol. 50. Elsevier, pp. 65–74, 2018.","apa":"Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002"},"date_published":"2018-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions."}],"title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","status":"public","intvolume":" 50","_id":"555","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","month":"06","quality_controlled":"1","isi":1,"external_id":{"isi":["000443661300011"]},"main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2017.12.002","publist_id":"7259","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","year":"2018","date_created":"2018-12-11T11:47:09Z","date_updated":"2023-09-11T14:07:03Z","volume":50,"author":[{"full_name":"Richter, Ralf","last_name":"Richter","first_name":"Ralf"},{"full_name":"Baranova, Natalia","last_name":"Baranova","first_name":"Natalia","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Day, Anthony","first_name":"Anthony","last_name":"Day"},{"last_name":"Kwok","first_name":"Jessica","full_name":"Kwok, Jessica"}]},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"_id":"448","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","ddc":["576"],"status":"public","pubrep_id":"969","file":[{"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","access_level":"open_access","file_size":3730583,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4731","date_updated":"2020-07-14T12:46:30Z","date_created":"2018-12-12T10:09:08Z","checksum":"874953136ac125e65f37971d3cabc5b7"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"05","citation":{"chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0459-1","ieee":"M. Harrison et al., “Hemimetabolous genomes reveal molecular basis of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566. doi:10.1038/s41559-017-0459-1"},"publication":"Nature Ecology and Evolution","page":"557-566","date_published":"2018-02-05T00:00:00Z","publist_id":"7375","file_date_updated":"2020-07-14T12:46:30Z","year":"2018","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","publisher":"Springer Nature","department":[{"_id":"BeVi"}],"publication_status":"published","related_material":{"record":[{"id":"9841","relation":"research_data","status":"public"}]},"author":[{"full_name":"Harrison, Mark","last_name":"Harrison","first_name":"Mark"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"last_name":"Robertson","first_name":"Hugh","full_name":"Robertson, Hugh"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"first_name":"Tristan","last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan"},{"full_name":"Chao, Hsu","last_name":"Chao","first_name":"Hsu"},{"full_name":"Childers, Christopher","first_name":"Christopher","last_name":"Childers"},{"full_name":"Dinh, Huyen","last_name":"Dinh","first_name":"Huyen"},{"last_name":"Doddapaneni","first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"full_name":"Greiner, Carolin","first_name":"Carolin","last_name":"Greiner"},{"full_name":"Han, Yi","first_name":"Yi","last_name":"Han"},{"full_name":"Hu, Haofu","first_name":"Haofu","last_name":"Hu"},{"full_name":"Hughes, Daniel","first_name":"Daniel","last_name":"Hughes"},{"last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"last_name":"Kemena","first_name":"Karsten","full_name":"Kemena, Karsten"},{"last_name":"Kremer","first_name":"Lukas","full_name":"Kremer, Lukas"},{"full_name":"Lee, Sandra","first_name":"Sandra","last_name":"Lee"},{"full_name":"López Ezquerra, Alberto","first_name":"Alberto","last_name":"López Ezquerra"},{"full_name":"Mallet, Ludovic","last_name":"Mallet","first_name":"Ludovic"},{"first_name":"Jose","last_name":"Monroy Kuhn","full_name":"Monroy Kuhn, Jose"},{"last_name":"Moser","first_name":"Annabell","full_name":"Moser, Annabell"},{"last_name":"Murali","first_name":"Shwetha","full_name":"Murali, Shwetha"},{"last_name":"Muzny","first_name":"Donna","full_name":"Muzny, Donna"},{"last_name":"Otani","first_name":"Saria","full_name":"Otani, Saria"},{"full_name":"Piulachs, Maria","last_name":"Piulachs","first_name":"Maria"},{"full_name":"Poelchau, Monica","first_name":"Monica","last_name":"Poelchau"},{"last_name":"Qu","first_name":"Jiaxin","full_name":"Qu, Jiaxin"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"full_name":"Wada Katsumata, Ayako","last_name":"Wada Katsumata","first_name":"Ayako"},{"first_name":"Kim","last_name":"Worley","full_name":"Worley, Kim"},{"full_name":"Xie, Qiaolin","last_name":"Xie","first_name":"Qiaolin"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","first_name":"Michael","last_name":"Poulsen"},{"full_name":"Gibbs, Richard","last_name":"Gibbs","first_name":"Richard"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"first_name":"Judith","last_name":"Korb","full_name":"Korb, Judith"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"}],"volume":2,"date_created":"2018-12-11T11:46:32Z","date_updated":"2023-09-11T14:10:57Z","month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000426559600026"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41559-017-0459-1","language":[{"iso":"eng"}]},{"publist_id":"6957","ec_funded":1,"file_date_updated":"2020-07-14T12:47:54Z","author":[{"last_name":"Oliveto","first_name":"Pietro","full_name":"Oliveto, Pietro"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"}],"volume":80,"date_created":"2018-12-11T11:48:09Z","date_updated":"2023-09-11T14:11:35Z","year":"2018","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Springer","publication_status":"published","month":"05","doi":"10.1007/s00453-017-0369-2","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000428239300010"]},"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"isi":1,"quality_controlled":"1","issue":"5","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"type":"journal_article","pubrep_id":"1014","file":[{"access_level":"open_access","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","creator":"system","content_type":"application/pdf","file_size":691245,"file_id":"4674","relation":"main_file","checksum":"7d92f5d7be81e387edeec4f06442791c","date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-12T10:08:14Z"}],"oa_version":"Published Version","_id":"723","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 80","status":"public","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","ddc":["576"],"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","citation":{"ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2."},"publication":"Algorithmica","page":"1604 - 1633"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"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. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998","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.","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,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","apa":"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. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998","mla":"Darrell, Trevor, et al. “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, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 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.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998."},"article_type":"original","page":"1029 - 1031","abstract":[{"lang":"eng","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."}],"issue":"5","type":"journal_article","file":[{"file_name":"2018_IEEE_Darrell.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":141724,"file_id":"7835","relation":"main_file","date_updated":"2020-07-14T12:46:03Z","date_created":"2020-05-14T12:50:48Z","checksum":"b19c75da06faf3291a3ca47dfa50ef63"}],"oa_version":"Published Version","_id":"321","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","ddc":["000"],"status":"public","intvolume":" 40","month":"05","doi":"10.1109/TPAMI.2018.2804998","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000428901200001"]},"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:03Z","publist_id":"7544","author":[{"last_name":"Darrell","first_name":"Trevor","full_name":"Darrell, Trevor"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Sebe, Nico","first_name":"Nico","last_name":"Sebe"},{"first_name":"Ying","last_name":"Wu","full_name":"Wu, Ying"},{"last_name":"Yan","first_name":"Yan","full_name":"Yan, Yan"}],"date_updated":"2023-09-11T14:07:54Z","date_created":"2018-12-11T11:45:48Z","volume":40,"year":"2018","publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}]},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"448"}]},"author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"first_name":"Hugh M.","last_name":"Robertson","full_name":"Robertson, Hugh M."},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"full_name":"Bitard-Feildel, Tristan","last_name":"Bitard-Feildel","first_name":"Tristan"},{"last_name":"Chao","first_name":"Hsu","full_name":"Chao, Hsu"},{"full_name":"Childers, Christopher P.","last_name":"Childers","first_name":"Christopher P."},{"full_name":"Dinh, Huyen","last_name":"Dinh","first_name":"Huyen"},{"full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni","first_name":"Harshavardhan"},{"first_name":"Shannon","last_name":"Dugan","full_name":"Dugan, Shannon"},{"last_name":"Gowin","first_name":"Johannes","full_name":"Gowin, Johannes"},{"full_name":"Greiner, Carolin","first_name":"Carolin","last_name":"Greiner"},{"full_name":"Han, Yi","first_name":"Yi","last_name":"Han"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"last_name":"Hughes","first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T."},{"last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"first_name":"Carsten","last_name":"Kemena","full_name":"Kemena, Carsten"},{"first_name":"Lukas P. M.","last_name":"Kremer","full_name":"Kremer, Lukas P. M."},{"full_name":"Lee, Sandra L.","first_name":"Sandra L.","last_name":"Lee"},{"full_name":"Lopez-Ezquerra, Alberto","first_name":"Alberto","last_name":"Lopez-Ezquerra"},{"full_name":"Mallet, Ludovic","first_name":"Ludovic","last_name":"Mallet"},{"full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn","first_name":"Jose M."},{"full_name":"Moser, Annabell","first_name":"Annabell","last_name":"Moser"},{"full_name":"Murali, Shwetha C.","first_name":"Shwetha C.","last_name":"Murali"},{"full_name":"Muzny, Donna M.","first_name":"Donna M.","last_name":"Muzny"},{"full_name":"Otani, Saria","first_name":"Saria","last_name":"Otani"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"full_name":"Poelchau, Monica","last_name":"Poelchau","first_name":"Monica"},{"first_name":"Jiaxin","last_name":"Qu","full_name":"Qu, Jiaxin"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"first_name":"Ayako","last_name":"Wada-Katsumata","full_name":"Wada-Katsumata, Ayako"},{"full_name":"Worley, Kim C.","last_name":"Worley","first_name":"Kim C."},{"last_name":"Xie","first_name":"Qiaolin","full_name":"Xie, Qiaolin"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"first_name":"Michael","last_name":"Poulsen","full_name":"Poulsen, Michael"},{"first_name":"Richard A.","last_name":"Gibbs","full_name":"Gibbs, Richard A."},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"full_name":"Richards, Stephen","first_name":"Stephen","last_name":"Richards"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"last_name":"Korb","first_name":"Judith","full_name":"Korb, Judith"},{"full_name":"Bornberg-Bauer, Erich","first_name":"Erich","last_name":"Bornberg-Bauer"}],"oa_version":"Published Version","date_updated":"2023-09-11T14:10:56Z","date_created":"2021-08-09T13:13:48Z","_id":"9841","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"}],"publisher":"Dryad","status":"public","title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"type":"research_data_reference","date_published":"2018-12-12T00:00:00Z","doi":"10.5061/dryad.51d4r","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"citation":{"ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.","ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. https://doi.org/10.5061/dryad.51d4r.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r."},"oa":1,"article_processing_charge":"No","month":"12","day":"12"},{"issue":"1","abstract":[{"lang":"eng","text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. "}],"alternative_title":["PPoPP"],"type":"conference","oa_version":"None","intvolume":" 53","title":"Harnessing epoch-based reclamation for efficient range queries","status":"public","_id":"397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2018-02-10T00:00:00Z","page":"14 - 27","citation":{"chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489"},"publist_id":"7430","volume":53,"date_created":"2018-12-11T11:46:14Z","date_updated":"2023-09-11T14:10:25Z","author":[{"first_name":"Maya","last_name":"Arbel Raviv","full_name":"Arbel Raviv, Maya"},{"full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"}],"publisher":"ACM","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2018","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1145/3178487.3178489","conference":{"name":"PPoPP: Principles and Practice of Parallel Programming","end_date":"2018-02-28","start_date":"2018-02-24","location":"Vienna, Austria"},"isi":1,"quality_controlled":"1","external_id":{"isi":["000446161100002"]}},{"date_created":"2018-12-11T11:44:16Z","date_updated":"2023-09-11T14:13:32Z","volume":25,"author":[{"last_name":"Chen","first_name":"Ting","full_name":"Chen, Ting"},{"full_name":"Kula, Bartosz","last_name":"Kula","first_name":"Bartosz"},{"id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","orcid":"0000-0002-4002-4686","first_name":"Balint","last_name":"Nagy","full_name":"Nagy, Balint"},{"full_name":"Barzan, Ruxandra","first_name":"Ruxandra","last_name":"Barzan"},{"full_name":"Gall, Andrea","last_name":"Gall","first_name":"Andrea"},{"last_name":"Ehrlich","first_name":"Ingrid","full_name":"Ehrlich, Ingrid"},{"full_name":"Kukley, Maria","last_name":"Kukley","first_name":"Maria"}],"publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Elsevier","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.","year":"2018","file_date_updated":"2020-07-14T12:46:03Z","publist_id":"8023","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2018.09.066","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000448219500005"]},"month":"10","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4461997,"access_level":"open_access","file_name":"2018_CellReports_Chen.pdf","checksum":"d9f74277fd57176e04732707d575cf08","date_created":"2018-12-17T12:42:57Z","date_updated":"2020-07-14T12:46:03Z","file_id":"5703","relation":"main_file"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","intvolume":" 25","_id":"32","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","date_published":"2018-10-23T00:00:00Z","page":"852 - 861.e7","publication":"Cell Reports","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.” Cell Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7.","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.","ieee":"T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.","apa":"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. Elsevier. https://doi.org/10.1016/j.celrep.2018.09.066","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. Cell Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066"},"day":"23","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"issue":"12","abstract":[{"lang":"eng","text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2019-02-06T08:49:52Z","date_updated":"2020-07-14T12:47:09Z","checksum":"687beea1d64c213f4cb9e3c29ec11a14","relation":"main_file","file_id":"5931","content_type":"application/pdf","file_size":1216437,"creator":"dernst","file_name":"2018_JournalExperMed_Reversat.pdf","access_level":"open_access"}],"intvolume":" 215","ddc":["570"],"title":"IgM's exit route","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5672","article_processing_charge":"No","has_accepted_license":"1","day":"20","scopus_import":"1","date_published":"2018-11-20T00:00:00Z","page":"2959-2961","citation":{"ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","apa":"Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","ama":"Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934","chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:10.1084/jem.20181934."},"publication":"Journal of Experimental Medicine","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:09Z","volume":215,"date_created":"2018-12-16T22:59:18Z","date_updated":"2023-09-11T14:12:06Z","author":[{"full_name":"Reversat, Anne","first_name":"Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"department":[{"_id":"MiSi"}],"publisher":"Rockefeller University Press","publication_status":"published","year":"2018","publication_identifier":{"issn":["00221007"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1084/jem.20181934","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"external_id":{"isi":["000451920600002"]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"398","year":"2018","publisher":"Elsevier","intvolume":" 13","department":[{"_id":"BeBi"}],"status":"public","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","publication_status":"published","author":[{"full_name":"Dodier, Philippe","last_name":"Dodier","first_name":"Philippe"},{"full_name":"Frischer, Josa","first_name":"Josa","last_name":"Frischer"},{"last_name":"Wang","first_name":"Wei","full_name":"Wang, Wei"},{"full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger"},{"full_name":"Mallouhi, Ammar","first_name":"Ammar","last_name":"Mallouhi"},{"first_name":"Wolfgang","last_name":"Serles","full_name":"Serles, Wolfgang"},{"last_name":"Gruber","first_name":"Andreas","full_name":"Gruber, Andreas"},{"full_name":"Knosp, Engelbert","first_name":"Engelbert","last_name":"Knosp"},{"first_name":"Gerhard","last_name":"Bavinzski","full_name":"Bavinzski, Gerhard"}],"volume":13,"oa_version":"None","date_updated":"2023-09-11T14:12:33Z","date_created":"2018-12-11T11:46:15Z","type":"journal_article","publist_id":"7431","abstract":[{"text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices.","lang":"eng"}],"external_id":{"isi":["000432942700070"]},"citation":{"chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096"},"publication":"World Neurosurgery","page":"e568-e578","isi":1,"quality_controlled":"1","doi":"10.1016/j.wneu.2018.02.096","date_published":"2018-05-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","day":"01","month":"05"},{"date_published":"2018-04-01T00:00:00Z","citation":{"short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292.","chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society. American Mathematical Society, 2018. https://doi.org/10.1090/tran/7292.","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292","apa":"Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7292","ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions of the American Mathematical Society, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854."},"publication":"Transactions of the American Mathematical Society","page":"2825 - 2854","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"458","intvolume":" 370","title":"Incircular nets and confocal conics","status":"public","issue":"4","abstract":[{"lang":"eng","text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem."}],"type":"journal_article","doi":"10.1090/tran/7292","language":[{"iso":"eng"}],"external_id":{"isi":["000423197800019"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"month":"04","author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"last_name":"Bobenko","first_name":"Alexander","full_name":"Bobenko, Alexander"}],"volume":370,"date_created":"2018-12-11T11:46:35Z","date_updated":"2023-09-11T14:19:12Z","year":"2018","acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society","publication_status":"published","ec_funded":1,"publist_id":"7363"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","page":"284-290","publication":"Journal of Insect Physiology","citation":{"ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003","ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier, pp. 284–290, 2018.","apa":"Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90, doi:10.1016/j.jinsphys.2017.12.003.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology. Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003."},"abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"type":"journal_article","oa_version":"None","status":"public","title":"Individual- and ejaculate-specific sperm traits in ant males","intvolume":" 107","_id":"426","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.jinsphys.2017.12.003","quality_controlled":"1","isi":1,"external_id":{"isi":["000434751100034"]},"publist_id":"7397","date_updated":"2023-09-12T07:43:26Z","date_created":"2018-12-11T11:46:25Z","volume":107,"author":[{"full_name":"Metzler, Sina","last_name":"Metzler","first_name":"Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"}],"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Elsevier","year":"2018","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n"},{"day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2018-11-21T00:00:00Z","citation":{"ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.","chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2."},"page":"21-36","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5788","status":"public","title":"Infinite-duration poorman-bidding games","intvolume":" 11316","month":"11","publication_identifier":{"issn":["03029743"],"isbn":["9783030046118"]},"conference":{"name":"14th International Conference on Web and Internet Economics, WINE","end_date":"2018-12-17","location":"Oxford, UK","start_date":"2018-12-15"},"doi":"10.1007/978-3-030-04612-5_2","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1804.04372","open_access":"1"}],"external_id":{"isi":["000865933000002"],"arxiv":["1804.04372"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"}],"author":[{"last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"}],"date_updated":"2023-09-12T07:44:01Z","date_created":"2018-12-30T22:59:14Z","volume":11316,"year":"2018","publisher":"Springer","department":[{"_id":"ToHe"}]},{"volume":560,"date_updated":"2023-09-12T07:44:37Z","date_created":"2018-12-11T11:44:53Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"author":[{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"full_name":"Schur, Florian","first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"full_name":"Lyddon, Terri D","first_name":"Terri D","last_name":"Lyddon"},{"last_name":"Ricana","first_name":"Clifton L","full_name":"Ricana, Clifton L"},{"last_name":"Wagner","first_name":"Jonathan M","full_name":"Wagner, Jonathan M"},{"full_name":"Perilla, Juan R","first_name":"Juan R","last_name":"Perilla"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"first_name":"Marc C","last_name":"Johnson","full_name":"Johnson, Marc C"},{"full_name":"Pornillos, Owen","first_name":"Owen","last_name":"Pornillos"},{"last_name":"Vogt","first_name":"Volker","full_name":"Vogt, Volker"}],"publisher":"Nature Publishing Group","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"year":"2018","language":[{"iso":"eng"}],"doi":"10.1038/s41586-018-0396-4","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"publication_identifier":{"eissn":["1476-4687"]},"month":"08","oa_version":"Submitted Version","intvolume":" 560","title":"Inositol phosphates are assembly co-factors for HIV-1","status":"public","_id":"150","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"7719","abstract":[{"lang":"eng","text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1."}],"type":"journal_article","date_published":"2018-08-29T00:00:00Z","page":"509–512","article_type":"original","citation":{"apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4","ieee":"R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4."},"publication":"Nature","article_processing_charge":"No","day":"29","scopus_import":"1"},{"publist_id":"7576","acknowledgement":"The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation.","year":"2018","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"AIMS","author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"}],"date_created":"2018-12-11T11:45:43Z","date_updated":"2023-09-12T07:45:37Z","volume":38,"month":"06","external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1706.03062","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.3934/dcds.2018120","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves."}],"issue":"6","_id":"303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Introduction to tropical series and wave dynamic on them","status":"public","intvolume":" 38","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Discrete and Continuous Dynamical Systems- Series A","citation":{"ama":"Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120","ista":"Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.","ieee":"N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018.","apa":"Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.","short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120."},"page":"2827 - 2849","date_published":"2018-06-01T00:00:00Z"},{"citation":{"short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, Vol. 31. Neural Information Processing Systems Foundation, 2018.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31."},"publication":"Advances in Neural Information Processing Systems","date_published":"2018-06-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"06","intvolume":" 31","status":"public","title":"Boosting black box variational inference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14202","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"quality_controlled":"1","external_id":{"arxiv":["1806.02185"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Montreal, Canada","start_date":"2018-12-03","end_date":"2018-12-08","name":"NeurIPS: Neural Information Processing Systems"},"publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"month":"06","department":[{"_id":"FrLo"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","year":"2018","volume":31,"date_updated":"2023-09-13T07:38:24Z","date_created":"2023-08-22T14:15:40Z","author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"first_name":"Gideon","last_name":"Dresdner","full_name":"Dresdner, Gideon"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"full_name":"Valera, Isabel","last_name":"Valera","first_name":"Isabel"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"extern":"1"},{"month":"04","language":[{"iso":"eng"}],"conference":{"end_date":"2018-04-11","start_date":"2018-04-09","location":"Playa Blanca, Lanzarote","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1708.01733"]},"main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"extern":"1","date_created":"2023-08-22T14:15:20Z","date_updated":"2023-09-13T07:52:40Z","volume":84,"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"full_name":"Ghosh, Joydeep","last_name":"Ghosh","first_name":"Joydeep"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2018","day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-15T00:00:00Z","page":"464-472","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","citation":{"ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72."},"abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","title":"Boosting variational inference: An optimization perspective","status":"public","intvolume":" 84","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14201"},{"author":[{"full_name":"Fortuin, Vincent","first_name":"Vincent","last_name":"Fortuin"},{"full_name":"Hüser, Matthias","first_name":"Matthias","last_name":"Hüser"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Strathmann, Heiko","last_name":"Strathmann","first_name":"Heiko"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"oa_version":"Preprint","date_created":"2023-08-22T14:12:48Z","date_updated":"2023-09-13T06:35:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14198","year":"2018","department":[{"_id":"FrLo"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"extern":"1","type":"conference","date_published":"2018-06-06T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","location":"New Orleans, LA, United States","start_date":"2019-05-06","end_date":"2019-05-09"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"oa":1,"external_id":{"arxiv":["1806.02199"]},"citation":{"ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018."},"publication":"International Conference on Learning Representations","quality_controlled":"1","article_processing_charge":"No","month":"06","day":"06"},{"extern":"1","date_created":"2023-08-22T14:16:01Z","date_updated":"2023-09-13T08:13:39Z","volume":80,"author":[{"full_name":"Yurtsever, Alp","first_name":"Alp","last_name":"Yurtsever"},{"first_name":"Olivier","last_name":"Fercoq","full_name":"Fercoq, Olivier"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2018","month":"07","language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"oa":1,"external_id":{"arxiv":["1804.08544"]},"abstract":[{"lang":"eng","text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework."}],"alternative_title":["PMLR"],"type":"conference","oa_version":"Preprint","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","status":"public","intvolume":" 80","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14203","day":"15","article_processing_charge":"No","date_published":"2018-07-15T00:00:00Z","page":"5727-5736","publication":"Proceedings of the 35th International Conference on Machine Learning","citation":{"chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736."}},{"type":"journal_article","abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"issue":"4","status":"public","title":"Introgression of a block of genome under infinitesimal selection","intvolume":" 209","_id":"282","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","page":"1279 - 1303","publication":"Genetics","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018."},"date_published":"2018-08-01T00:00:00Z","publist_id":"7617","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"year":"2018","date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","volume":209,"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"08","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000440014100020"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301018"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"108","intvolume":" 2018","title":"Inverted leftover hash lemma","status":"public","oa_version":"Submitted Version","type":"conference","alternative_title":["ISIT Proceedings"],"abstract":[{"text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.","lang":"eng"}],"citation":{"short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018."},"date_published":"2018-08-16T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"16","year":"2018","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"first_name":"Marciej","last_name":"Obremski","full_name":"Obremski, Marciej"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skorski","full_name":"Skorski, Maciej"}],"volume":2018,"date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:23:18Z","publist_id":"7946","oa":1,"external_id":{"isi":["000448139300368"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"quality_controlled":"1","isi":1,"doi":"10.1109/ISIT.2018.8437654","conference":{"name":"ISIT: International Symposium on Information Theory","location":"Vail, CO, USA","start_date":"2018-06-17 ","end_date":"2018-06-22"},"language":[{"iso":"eng"}],"month":"08"},{"date_published":"2018-07-01T00:00:00Z","page":"3198-3207","publication":"Proceedings of the 35th International Conference on Machine Learning","citation":{"ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"On matching pursuit and coordinate descent","status":"public","intvolume":" 80","_id":"14204","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"alternative_title":["PMLR"],"type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1803.09539"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"month":"07","date_created":"2023-08-22T14:16:25Z","date_updated":"2023-09-13T08:19:05Z","volume":80,"author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Raj, Anant","first_name":"Anant","last_name":"Raj"},{"first_name":"Sai Praneeth","last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"full_name":"Stich, Sebastian U.","first_name":"Sebastian U.","last_name":"Stich"},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}],"publication_status":"published","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","year":"2018","extern":"1"},{"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":10981,"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-09-13T08:45:09Z","related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"publist_id":"7761","file_date_updated":"2020-07-14T12:45:04Z","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000491481600005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_5","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-14"},"month":"07","intvolume":" 10981","status":"public","title":"Layered Concurrent Programs","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"160","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_LNCS_Kragl.pdf","creator":"dernst","file_size":1603844,"content_type":"application/pdf","file_id":"5705","relation":"main_file","checksum":"c64fff560fe5a7532ec10626ad1c215e","date_created":"2018-12-17T12:52:12Z","date_updated":"2020-07-14T12:45:04Z"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"page":"79 - 102","citation":{"ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5."},"date_published":"2018-07-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18"}]