[{"doi":"10.1063/1.4983703","language":[{"iso":"eng"}],"external_id":{"isi":["000405089400047"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1704.03684","open_access":"1"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00219606"]},"month":"06","author":[{"last_name":"Shepperson","first_name":"Benjamin","full_name":"Shepperson, Benjamin"},{"last_name":"Chatterley","first_name":"Adam","full_name":"Chatterley, Adam"},{"first_name":"Anders","last_name":"Søndergaard","full_name":"Søndergaard, Anders"},{"last_name":"Christiansen","first_name":"Lars","full_name":"Christiansen, Lars"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"}],"volume":147,"date_created":"2018-12-11T11:49:36Z","date_updated":"2024-02-28T13:02:26Z","year":"2017","publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"publication_status":"published","publist_id":"6403","article_number":"013946","date_published":"2017-06-01T00:00:00Z","citation":{"ama":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 2017;147(1). doi:10.1063/1.4983703","ieee":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, and H. Stapelfeldt, “Strongly aligned molecules inside helium droplets in the near-adiabatic regime,” The Journal of Chemical Physics, vol. 147, no. 1. AIP Publishing, 2017.","apa":"Shepperson, B., Chatterley, A., Søndergaard, A., Christiansen, L., Lemeshko, M., & Stapelfeldt, H. (2017). Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4983703","ista":"Shepperson B, Chatterley A, Søndergaard A, Christiansen L, Lemeshko M, Stapelfeldt H. 2017. Strongly aligned molecules inside helium droplets in the near-adiabatic regime. The Journal of Chemical Physics. 147(1), 013946.","short":"B. Shepperson, A. Chatterley, A. Søndergaard, L. Christiansen, M. Lemeshko, H. Stapelfeldt, The Journal of Chemical Physics 147 (2017).","mla":"Shepperson, Benjamin, et al. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics, vol. 147, no. 1, 013946, AIP Publishing, 2017, doi:10.1063/1.4983703.","chicago":"Shepperson, Benjamin, Adam Chatterley, Anders Søndergaard, Lars Christiansen, Mikhail Lemeshko, and Henrik Stapelfeldt. “Strongly Aligned Molecules inside Helium Droplets in the Near-Adiabatic Regime.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4983703."},"publication":"The Journal of Chemical Physics","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"996","intvolume":" 147","status":"public","title":"Strongly aligned molecules inside helium droplets in the near-adiabatic regime","issue":"1","abstract":[{"lang":"eng","text":"Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. "}],"type":"journal_article"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-08-01T00:00:00Z","publication":" Journal of Mathematical Physics","citation":{"short":"A. Deuchert, Journal of Mathematical Physics 58 (2017).","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:10.1063/1.4996580.","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4996580.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 2017;58(8). doi:10.1063/1.4996580","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing, 2017.","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 58(8), 081901."},"abstract":[{"lang":"eng","text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"}],"issue":"8","type":"journal_article","oa_version":"Submitted Version","_id":"912","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A lower bound for the BCS functional with boundary conditions at infinity","intvolume":" 58","month":"08","publication_identifier":{"issn":["00222488"]},"doi":"10.1063/1.4996580","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"external_id":{"isi":["000409197200015"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"ec_funded":1,"publist_id":"6531","article_number":"081901","author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:49:10Z","date_updated":"2024-02-28T13:07:56Z","volume":58,"year":"2017","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"RoSe"}]},{"_id":"1029","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 12","ddc":["570"],"status":"public","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","pubrep_id":"800","file":[{"access_level":"open_access","file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","content_type":"application/pdf","file_size":3429381,"creator":"system","relation":"main_file","file_id":"4772","date_updated":"2018-12-12T10:09:47Z","date_created":"2018-12-12T10:09:47Z"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}],"citation":{"mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066"},"publication":"PLoS One","date_published":"2017-03-16T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"16","year":"2017","publisher":"Public Library of Science","department":[{"_id":"ToBo"}],"publication_status":"published","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5556"},{"relation":"dissertation_contains","status":"public","id":"6392"}]},"author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6549-4177","first_name":"Martin","last_name":"Lukacisin","full_name":"Lukacisin, Martin"},{"last_name":"Landon","first_name":"Matthieu","full_name":"Landon, Matthieu"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"volume":12,"date_created":"2018-12-11T11:49:46Z","date_updated":"2024-03-28T23:30:04Z","article_number":"e0174066","publist_id":"6361","file_date_updated":"2018-12-12T10:09:47Z","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":["000396318300121"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0174066","language":[{"iso":"eng"}],"publication_identifier":{"issn":["19326203"]},"month":"03"},{"publication_identifier":{"issn":["10747613"]},"day":"18","month":"04","scopus_import":1,"date_published":"2017-04-18T00:00:00Z","doi":"10.1016/j.immuni.2017.04.006","language":[{"iso":"eng"}],"citation":{"chicago":"Assen, Frank P, and Michael K Sixt. “The Dynamic Cytokine Niche.” Immunity. Cell Press, 2017. https://doi.org/10.1016/j.immuni.2017.04.006.","short":"F.P. Assen, M.K. Sixt, Immunity 46 (2017) 519–520.","mla":"Assen, Frank P., and Michael K. Sixt. “The Dynamic Cytokine Niche.” Immunity, vol. 46, no. 4, Cell Press, 2017, pp. 519–20, doi:10.1016/j.immuni.2017.04.006.","apa":"Assen, F. P., & Sixt, M. K. (2017). The dynamic cytokine niche. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2017.04.006","ieee":"F. P. Assen and M. K. Sixt, “The dynamic cytokine niche,” Immunity, vol. 46, no. 4. Cell Press, pp. 519–520, 2017.","ista":"Assen FP, Sixt MK. 2017. The dynamic cytokine niche. Immunity. 46(4), 519–520.","ama":"Assen FP, Sixt MK. The dynamic cytokine niche. Immunity. 2017;46(4):519-520. doi:10.1016/j.immuni.2017.04.006"},"publication":"Immunity","page":"519 - 520","quality_controlled":"1","issue":"4","publist_id":"7065","abstract":[{"lang":"eng","text":"Immune cells communicate using cytokine signals, but the quantitative rules of this communication aren't clear. In this issue of Immunity, Oyler-Yaniv et al. (2017) suggest that the distribution of a cytokine within a lymphatic organ is primarily governed by the local density of cells consuming it."}],"type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"author":[{"last_name":"Assen","first_name":"Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"volume":46,"oa_version":"None","date_created":"2018-12-11T11:47:47Z","date_updated":"2024-03-28T23:30:09Z","_id":"664","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 46","department":[{"_id":"MiSi"}],"publisher":"Cell Press","status":"public","title":"The dynamic cytokine niche","publication_status":"published"},{"author":[{"first_name":"Hikari","last_name":"Ukai","full_name":"Ukai, Hikari"},{"full_name":"Kawahara, Aiko","last_name":"Kawahara","first_name":"Aiko"},{"first_name":"Keiko","last_name":"Hirayama","full_name":"Hirayama, Keiko"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"},{"full_name":"Aino, Shotaro","first_name":"Shotaro","last_name":"Aino"},{"full_name":"Miyabe, Masahiro","last_name":"Miyabe","first_name":"Masahiro"},{"full_name":"Wakita, Ken","first_name":"Ken","last_name":"Wakita"},{"full_name":"Oogi, Ryohei","last_name":"Oogi","first_name":"Ryohei"},{"full_name":"Kasayuki, Michiyo","last_name":"Kasayuki","first_name":"Michiyo"},{"first_name":"Shihomi","last_name":"Kawashima","full_name":"Kawashima, Shihomi"},{"full_name":"Sugimoto, Shunichi","last_name":"Sugimoto","first_name":"Shunichi"},{"full_name":"Chikamatsu, Kanako","last_name":"Chikamatsu","first_name":"Kanako"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"full_name":"Koga, Tsuneyuki","last_name":"Koga","first_name":"Tsuneyuki"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Takai, Toshiyuki","last_name":"Takai","first_name":"Toshiyuki"},{"full_name":"Ito, Isao","first_name":"Isao","last_name":"Ito"}],"related_material":{"record":[{"id":"51","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:47:54Z","date_updated":"2024-03-28T23:30:12Z","volume":12,"year":"2017","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:40Z","publist_id":"7034","article_number":"e0179377","doi":"10.1371/journal.pone.0179377","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"},"quality_controlled":"1","month":"06","publication_identifier":{"issn":["19326203"]},"pubrep_id":"897","file":[{"access_level":"open_access","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","creator":"system","content_type":"application/pdf","file_size":5798454,"file_id":"4934","relation":"main_file","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","date_created":"2018-12-12T10:12:16Z","date_updated":"2020-07-14T12:47:40Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"682","title":"PirB regulates asymmetries in hippocampal circuitry","ddc":["571"],"status":"public","intvolume":" 12","abstract":[{"lang":"eng","text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry."}],"issue":"6","type":"journal_article","date_published":"2017-06-01T00:00:00Z","publication":"PLoS One","citation":{"ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377."},"article_type":"original","day":"01","has_accepted_license":"1","scopus_import":1},{"file_date_updated":"2019-01-18T09:39:55Z","ec_funded":1,"publist_id":"6362","author":[{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Kainrath"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva"},{"full_name":"Distel, Martin","last_name":"Distel","first_name":"Martin"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"},{"status":"public","relation":"part_of_dissertation","id":"7680"}]},"date_created":"2018-12-11T11:49:46Z","date_updated":"2024-03-28T23:30:13Z","volume":56,"year":"2017","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publisher":"Wiley-Blackwell","month":"03","publication_identifier":{"issn":["14337851"]},"doi":"10.1002/anie.201611998","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":{"isi":["000398154000038"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets [do not use to be deleted]"}],"abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"issue":"16","type":"journal_article","file":[{"success":1,"date_updated":"2019-01-18T09:39:55Z","date_created":"2019-01-18T09:39:55Z","file_id":"5845","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2614942,"access_level":"open_access","file_name":"2017_communications_Kainrath.pdf"}],"oa_version":"Published Version","_id":"1028","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","ddc":["540"],"intvolume":" 56","day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-03-20T00:00:00Z","publication":"Angewandte Chemie - International Edition","citation":{"ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998."},"page":"4608-4611"},{"doi":"10.1007/978-1-4939-6831-2_1","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"}],"quality_controlled":"1","publication_identifier":{"issn":["10643745"]},"month":"03","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"539"}]},"author":[{"full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426","first_name":"Andrej","last_name":"Hurny"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"volume":1569,"date_created":"2018-12-11T11:49:45Z","date_updated":"2024-03-28T23:30:17Z","year":"2017","publisher":"Springer","department":[{"_id":"EvBe"}],"publication_status":"published","publist_id":"6369","file_date_updated":"2019-10-15T07:47:05Z","date_published":"2017-03-17T00:00:00Z","citation":{"ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1."},"publication":"Auxins and Cytokinins in Plant Biology","page":"1 - 29","has_accepted_license":"1","day":"17","scopus_import":1,"pubrep_id":"1019","file":[{"date_updated":"2019-10-15T07:47:05Z","date_created":"2018-12-12T10:14:18Z","relation":"main_file","file_id":"5068","content_type":"application/pdf","file_size":840646,"creator":"system","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"1024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 1569","title":"Methodological advances in auxin and cytokinin biology","ddc":["575"],"status":"public","abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"type":"journal_article","alternative_title":["Methods in Molecular Biology"]},{"publication_identifier":{"issn":["00219738"]},"month":"06","project":[{"name":"The biochemical basis of PAR polarization","call_identifier":"FWF","_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"external_id":{"pmid":["28504646"]},"language":[{"iso":"eng"}],"doi":"10.1172/JCI80631","publist_id":"7038","publisher":"American Society for Clinical Investigation","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","year":"2017","volume":127,"date_created":"2018-12-11T11:47:53Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"record":[{"id":"12401","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Ebner","first_name":"Florian","full_name":"Ebner, Florian"},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan"},{"full_name":"Ivin, Masa","first_name":"Masa","last_name":"Ivin"},{"full_name":"Kratochvill, Franz","first_name":"Franz","last_name":"Kratochvill"},{"first_name":"Nina","last_name":"Gratz","full_name":"Gratz, Nina"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"first_name":"Andreas","last_name":"Villunger","full_name":"Villunger, Andreas"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Kovarik, Pavel","last_name":"Kovarik","first_name":"Pavel"}],"scopus_import":1,"day":"01","page":"2051 - 2065","citation":{"chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2017. https://doi.org/10.1172/JCI80631.","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” The Journal of Clinical Investigation, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:10.1172/JCI80631.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI80631","ieee":"F. Ebner et al., “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” The Journal of Clinical Investigation, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 2017;127(6):2051-2065. doi:10.1172/JCI80631"},"publication":"The Journal of Clinical Investigation","date_published":"2017-06-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"intvolume":" 127","status":"public","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"679","oa_version":"Submitted Version"},{"doi":"10.1242/dev.144964","language":[{"iso":"eng"}],"external_id":{"pmid":["28512197"]},"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,"quality_controlled":"1","month":"05","publication_identifier":{"issn":["09501991"]},"author":[{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel"},{"last_name":"Veldhuis","first_name":"Jim","full_name":"Veldhuis, Jim"},{"full_name":"Barone, Vanessa","last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","first_name":"Daniel","full_name":"Capek, Daniel"},{"full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","last_name":"Maître"},{"first_name":"Wayne","last_name":"Brodland","full_name":"Brodland, Wayne"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:47:52Z","date_updated":"2024-03-28T23:30:26Z","volume":144,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"Bio"},{"_id":"CaHe"}],"publisher":"Company of Biologists","file_date_updated":"2020-07-14T12:47:39Z","publist_id":"7047","date_published":"2017-05-15T00:00:00Z","publication":"Development","citation":{"chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144964.","mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” Development, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:10.1242/dev.144964.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","ieee":"G. Krens et al., “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” Development, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., & Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.144964","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 2017;144(10):1798-1806. doi:10.1242/dev.144964"},"article_type":"original","page":"1798 - 1806","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"oa_version":"Published Version","file":[{"file_size":8194516,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Development_Krens.pdf","checksum":"bc25125fb664706cdf180e061429f91d","date_updated":"2020-07-14T12:47:39Z","date_created":"2019-09-24T06:56:22Z","relation":"main_file","file_id":"6905"}],"_id":"676","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","status":"public","ddc":["570"],"intvolume":" 144","abstract":[{"lang":"eng","text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation."}],"issue":"10","type":"journal_article"},{"has_accepted_license":"1","day":"25","scopus_import":1,"date_published":"2017-07-25T00:00:00Z","citation":{"ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100."},"publication":"eLife","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","creator":"system","content_type":"application/pdf","file_size":2092088,"file_id":"4975","relation":"main_file","checksum":"6b908b5db9f61f6820ebd7f8fa815571","date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:54Z"},{"file_size":3428681,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","date_created":"2018-12-12T10:12:55Z","checksum":"ca21530389b720243552678125fdba35","relation":"main_file","file_id":"4976"}],"pubrep_id":"890","intvolume":" 6","ddc":["576"],"status":"public","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","_id":"704","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2050084X"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.7554/eLife.25100","quality_controlled":"1","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"},"publist_id":"6990","file_date_updated":"2020-07-14T12:47:48Z","article_number":"e25100","volume":6,"date_created":"2018-12-11T11:48:01Z","date_updated":"2024-03-28T23:30:28Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5564"},{"id":"26","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Steinrück, Magdalena","first_name":"Magdalena","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1229-9719"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017"},{"month":"07","publication_identifier":{"issn":["1553734X"]},"quality_controlled":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"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"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1005609","article_number":"e1005609","file_date_updated":"2020-07-14T12:47:46Z","publist_id":"7004","ec_funded":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2017","date_updated":"2024-03-28T23:30:28Z","date_created":"2018-12-11T11:47:58Z","volume":13,"author":[{"orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9849"},{"id":"9850","status":"public","relation":"research_data"},{"id":"9851","status":"public","relation":"research_data"},{"id":"9852","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"scopus_import":1,"day":"18","has_accepted_license":"1","article_type":"original","publication":"PLoS Computational Biology","citation":{"ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."},"date_published":"2017-07-18T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"issue":"7","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","status":"public","ddc":["576"],"intvolume":" 13","_id":"696","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","access_level":"open_access","creator":"system","file_size":3775716,"content_type":"application/pdf","file_id":"5117","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:15:01Z","checksum":"9143c290fa6458ed2563bff4b295554a"}],"pubrep_id":"894"},{"_id":"1027","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 46","ddc":["570"],"status":"public","title":"Toward a quantitative understanding of antibiotic resistance evolution","pubrep_id":"801","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5846","date_created":"2019-01-18T09:57:57Z","date_updated":"2019-01-18T09:57:57Z","success":1,"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":858338,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"citation":{"ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013."},"publication":"Current Opinion in Biotechnology","page":"90 - 97","article_type":"original","date_published":"2017-08-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","year":"2017","department":[{"_id":"ToBo"}],"publisher":"Elsevier","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6263"}]},"author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"volume":46,"date_created":"2018-12-11T11:49:45Z","date_updated":"2024-03-28T23:30:29Z","ec_funded":1,"publist_id":"6364","file_date_updated":"2019-01-18T09:57:57Z","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":["000408077400015"]},"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.copbio.2017.02.013","language":[{"iso":"eng"}],"month":"08"},{"conference":{"end_date":"2017-07-28","start_date":"2017-07-24","location":"Heidelberg, Germany","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-319-63390-9_3","language":[{"iso":"eng"}],"external_id":{"arxiv":["1705.00317"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"oa":1,"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"month":"01","publication_identifier":{"isbn":["978-331963389-3"]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir","last_name":"Goharshady","full_name":"Goharshady, Amir"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"7014"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_updated":"2024-03-28T23:30:33Z","date_created":"2018-12-11T11:47:39Z","volume":10427,"year":"2017","publication_status":"published","editor":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","ec_funded":1,"publist_id":"7149","date_published":"2017-01-01T00:00:00Z","citation":{"ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst case analysis of recursive programs. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:41-63. doi:10.1007/978-3-319-63390-9_3","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst case analysis of recursive programs,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 41–63.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2017). Non-polynomial worst case analysis of recursive programs. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 41–63). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_3","ista":"Chatterjee K, Fu H, Goharshady AK. 2017. Non-polynomial worst case analysis of recursive programs. CAV: Computer Aided Verification, LNCS, vol. 10427, 41–63.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 41–63.","mla":"Chatterjee, Krishnendu, et al. Non-Polynomial Worst Case Analysis of Recursive Programs. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 41–63, doi:10.1007/978-3-319-63390-9_3.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst Case Analysis of Recursive Programs.” edited by Rupak Majumdar and Viktor Kunčak, 10427:41–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_3."},"page":"41 - 63","day":"01","article_processing_charge":"No","scopus_import":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"639","title":"Non-polynomial worst case analysis of recursive programs","status":"public","intvolume":" 10427","abstract":[{"text":"We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"]},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"59 - 66","citation":{"apa":"Chatterjee, K., Goharshady, A. K., & Pavlogiannis, A. (2017). JTDec: A tool for tree decompositions in soot. In D. D’Souza (Ed.) (Vol. 10482, pp. 59–66). Presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India: Springer. https://doi.org/10.1007/978-3-319-68167-2_4","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pavlogiannis, “JTDec: A tool for tree decompositions in soot,” presented at the ATVA: Automated Technology for Verification and Analysis, Pune, India, 2017, vol. 10482, pp. 59–66.","ista":"Chatterjee K, Goharshady AK, Pavlogiannis A. 2017. JTDec: A tool for tree decompositions in soot. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 10482, 59–66.","ama":"Chatterjee K, Goharshady AK, Pavlogiannis A. JTDec: A tool for tree decompositions in soot. In: D’Souza D, ed. Vol 10482. Springer; 2017:59-66. doi:10.1007/978-3-319-68167-2_4","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. “JTDec: A Tool for Tree Decompositions in Soot.” edited by Deepak D’Souza, 10482:59–66. Springer, 2017. https://doi.org/10.1007/978-3-319-68167-2_4.","short":"K. Chatterjee, A.K. Goharshady, A. Pavlogiannis, in:, D. D’Souza (Ed.), Springer, 2017, pp. 59–66.","mla":"Chatterjee, Krishnendu, et al. JTDec: A Tool for Tree Decompositions in Soot. Edited by Deepak D’Souza, vol. 10482, Springer, 2017, pp. 59–66, doi:10.1007/978-3-319-68167-2_4."},"date_published":"2017-01-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs."}],"status":"public","title":"JTDec: A tool for tree decompositions in soot","ddc":["005"],"intvolume":" 10482","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"949","file":[{"date_created":"2018-12-12T10:10:45Z","date_updated":"2020-07-14T12:48:16Z","checksum":"a0d9f5f94dc594c4e71e78525c9942f1","file_id":"4835","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":948514,"file_name":"IST-2017-845-v1+1_2017_Chatterjee_JTDec.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","pubrep_id":"845","month":"01","publication_identifier":{"issn":["03029743"]},"quality_controlled":"1","isi":1,"project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"external_id":{"isi":["000723567800004"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2017-10-06","location":"Pune, India","start_date":"2017-10-03"},"doi":"10.1007/978-3-319-68167-2_4","file_date_updated":"2020-07-14T12:48:16Z","publist_id":"6468","ec_funded":1,"publication_status":"published","editor":[{"last_name":"D'Souza","first_name":"Deepak","full_name":"D'Souza, Deepak"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2017","date_created":"2018-12-11T11:49:22Z","date_updated":"2024-03-28T23:30:35Z","volume":10482,"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Goharshady, Amir","last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo."}],"intvolume":" 19","status":"public","title":"Friction forces position the neural anlage","_id":"661","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"27","page":"306 - 317","citation":{"ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","ieee":"M. Smutny et al., “Friction forces position the neural anlage,” Nature Cell Biology, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3492","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. Nature Cell Biology. 2017;19:306-317. doi:10.1038/ncb3492","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3492.","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” Nature Cell Biology, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:10.1038/ncb3492.","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317."},"publication":"Nature Cell Biology","date_published":"2017-03-27T00:00:00Z","ec_funded":1,"publist_id":"7074","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"year":"2017","volume":19,"date_updated":"2024-03-28T23:30:39Z","date_created":"2018-12-11T11:47:46Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"50"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","first_name":"Michael","last_name":"Smutny"},{"full_name":"Ákos, Zsuzsa","first_name":"Zsuzsa","last_name":"Ákos"},{"full_name":"Grigolon, Silvia","first_name":"Silvia","last_name":"Grigolon"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"full_name":"Capek, Daniel","first_name":"Daniel","last_name":"Capek","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940"},{"first_name":"Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"first_name":"Ekaterina","last_name":"Papusheva","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","full_name":"Papusheva, Ekaterina"},{"full_name":"Tada, Masazumi","last_name":"Tada","first_name":"Masazumi"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"full_name":"Vicsek, Tamás","first_name":"Tamás","last_name":"Vicsek"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"publication_identifier":{"issn":["14657392"]},"month":"03","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"},{"_id":"252ABD0A-B435-11E9-9278-68D0E5697425","grant_number":"I 930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"pmid":["28346437"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc5635970"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1038/ncb3492"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2017.09.014","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Cell segregation in gastrulation: the role of cell fate specification","call_identifier":"FWF","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","grant_number":"I2058"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000413443700011"]},"publication_identifier":{"issn":["15345807"]},"month":"10","volume":43,"date_updated":"2024-03-28T23:30:39Z","date_created":"2018-12-11T11:48:13Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa","full_name":"Barone, Vanessa"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz"},{"full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Cell Press","publication_status":"published","year":"2017","publist_id":"6934","ec_funded":1,"date_published":"2017-10-23T00:00:00Z","page":"198 - 211","citation":{"mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.","chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","ieee":"V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.014"},"publication":"Developmental Cell","article_processing_charge":"No","day":"23","scopus_import":"1","oa_version":"None","intvolume":" 43","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"735","issue":"2","abstract":[{"lang":"eng","text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo."}],"type":"journal_article"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"960","intvolume":" 11","ddc":["570"],"status":"public","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","pubrep_id":"830","oa_version":"Published Version","file":[{"checksum":"dc1f5a475b918d09a0f9f587400b1626","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:09:40Z","file_id":"4764","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2153858,"access_level":"open_access","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf"}],"type":"journal_article","abstract":[{"text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.","lang":"eng"}],"citation":{"chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176"},"publication":"Frontiers in Cellular Neuroscience","date_published":"2017-06-28T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"28","year":"2017","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"publisher":"Frontiers Research Foundation","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9962"}]},"author":[{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen"},{"last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","full_name":"Düllberg, Christian F"},{"full_name":"Mieck, Christine","last_name":"Mieck","first_name":"Christine","orcid":"0000-0003-1919-7416","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"volume":11,"date_updated":"2024-03-28T23:30:41Z","date_created":"2018-12-11T11:49:25Z","article_number":"176","publist_id":"6445","ec_funded":1,"file_date_updated":"2020-07-14T12:48:16Z","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":{"isi":["000404486700001"]},"oa":1,"project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25985A36-B435-11E9-9278-68D0E5697425","grant_number":"T00817-B21","name":"The biochemical basis of PAR polarization","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.3389/fncel.2017.00176","language":[{"iso":"eng"}],"publication_identifier":{"issn":["16625102"]},"month":"06"},{"doi":"10.1021/acssynbio.6b00013","date_published":"2016-05-05T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107. doi:10.1021/acssynbio.6b00013","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., & Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00013","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:10.1021/acssynbio.6b00013.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology. American Chemical Society, 2016. https://doi.org/10.1021/acssynbio.6b00013."},"publication":"ACS Synthetic Biology","page":"1098 - 1107","quality_controlled":"1","month":"05","day":"05","author":[{"full_name":"Gnügge, Robert","first_name":"Robert","last_name":"Gnügge"},{"first_name":"Lekshmi","last_name":"Dharmarajan","full_name":"Dharmarajan, Lekshmi"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"oa_version":"None","volume":5,"date_created":"2018-12-11T11:49:40Z","date_updated":"2021-01-12T06:47:37Z","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","_id":"1008","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"American Chemical Society","intvolume":" 5","department":[{"_id":"CaGu"}],"status":"public","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","publication_status":"published","issue":"10","publist_id":"6390","abstract":[{"text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.25.","mla":"Chatterjee, Krishnendu, et al. Conditionally Optimal Algorithms for Generalized Büchi Games. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.25.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 25.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.25","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland, 2016, vol. 58.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.25"},"date_published":"2016-08-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m > n^{1.5}. ","lang":"eng"}],"_id":"1068","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000","004","006"],"title":"Conditionally optimal algorithms for generalized Büchi Games","intvolume":" 58","pubrep_id":"779","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5187","date_created":"2018-12-12T10:16:02Z","date_updated":"2018-12-12T10:16:02Z","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","access_level":"open_access","file_size":632786,"content_type":"application/pdf","creator":"system"}],"month":"08","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"conference":{"end_date":"2016-08-26","location":"Krakow, Poland","start_date":"2016-08-22","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"doi":"10.4230/LIPIcs.MFCS.2016.25","language":[{"iso":"eng"}],"article_number":"25","file_date_updated":"2018-12-12T10:16:02Z","publist_id":"6317","ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307","year":"2016","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"date_updated":"2023-02-14T10:11:07Z","date_created":"2018-12-11T11:49:58Z","volume":58},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.100","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ICALP.2016.100","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.100.","mla":"Chonev, Ventsislav K., et al. On the Skolem Problem for Continuous Linear Dynamical Systems. Vol. 55, 100, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ICALP.2016.100.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016."},"date_published":"2016-08-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers."}],"intvolume":" 55","status":"public","title":"On the skolem problem for continuous linear dynamical systems","ddc":["004","006"],"_id":"1069","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","file_size":521415,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","date_updated":"2018-12-12T10:16:26Z","date_created":"2018-12-12T10:16:26Z","file_id":"5213","relation":"main_file"}],"pubrep_id":"778","month":"08","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","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"},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2016.100","conference":{"end_date":"2016-07-15","location":"Rome, Italy","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming"},"article_number":"100","publist_id":"6314","ec_funded":1,"file_date_updated":"2018-12-12T10:16:26Z","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","publication_status":"published","acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and ERC Advanced Grant (267989: QUAREM).","year":"2016","volume":55,"date_created":"2018-12-11T11:49:59Z","date_updated":"2021-01-12T06:48:03Z","author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev","full_name":"Chonev, Ventsislav K"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}]},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","apa":"Chatterjee, K., & Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2016.98","ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ICALP.2016.98","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. https://doi.org/10.4230/LIPIcs.ICALP.2016.98.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Computation Tree Logic for Synchronization Properties. Vol. 55, 98, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ICALP.2016.98.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016."},"abstract":[{"text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"file_size":546133,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","access_level":"open_access","date_updated":"2018-12-12T10:08:52Z","date_created":"2018-12-12T10:08:52Z","relation":"main_file","file_id":"4714"}],"pubrep_id":"812","intvolume":" 55","ddc":["005"],"status":"public","title":"Computation tree logic for synchronization properties","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1070","month":"01","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2016.98","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12","location":"Rome, Italy","end_date":"2016-07-15"},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"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,"ec_funded":1,"publist_id":"6313","file_date_updated":"2018-12-12T10:08:52Z","article_number":"98","volume":55,"date_created":"2018-12-11T11:49:59Z","date_updated":"2021-01-12T06:48:03Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2016","acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n"},{"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":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","doi":"10.1038/celldisc.2016.18","language":[{"iso":"eng"}],"month":"07","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","year":"2016","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"last_name":"Łangowski","first_name":"Łukasz","full_name":"Łangowski, Łukasz"},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik"},{"first_name":"Hongjiang","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":2,"date_created":"2018-12-11T11:50:02Z","date_updated":"2021-01-12T06:48:08Z","article_number":"16018","ec_funded":1,"publist_id":"6299","file_date_updated":"2018-12-12T10:13:33Z","citation":{"mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery, vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2016;2. doi:10.1038/celldisc.2016.18","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., & Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. Nature Publishing Group. https://doi.org/10.1038/celldisc.2016.18","ieee":"Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” Cell Discovery, vol. 2. Nature Publishing Group, 2016."},"publication":"Cell Discovery","date_published":"2016-07-19T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"19","_id":"1081","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 2","ddc":["580"],"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","status":"public","pubrep_id":"757","oa_version":"Published Version","file":[{"file_name":"IST-2017-757-v1+1_celldisc201618.pdf","access_level":"open_access","creator":"system","file_size":5261671,"content_type":"application/pdf","file_id":"5017","relation":"main_file","date_created":"2018-12-12T10:13:33Z","date_updated":"2018-12-12T10:13:33Z"}],"type":"journal_article","abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}]},{"year":"2016","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","department":[{"_id":"CampIT"}],"publisher":"Computing in Cardiology","publication_status":"published","author":[{"full_name":"Rubel, Paul","last_name":"Rubel","first_name":"Paul"},{"full_name":"Pani, Danilo","last_name":"Pani","first_name":"Danilo"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"full_name":"Fayn, Jocelyne","last_name":"Fayn","first_name":"Jocelyne"},{"last_name":"Badilini","first_name":"Fabio","full_name":"Badilini, Fabio"},{"full_name":"Macfarlane, Peter","first_name":"Peter","last_name":"Macfarlane"},{"full_name":"Varri, Alpo","first_name":"Alpo","last_name":"Varri"}],"volume":43,"date_updated":"2022-03-04T07:34:45Z","date_created":"2022-03-03T10:43:10Z","publication_identifier":{"issn":["2325-887X"]},"month":"03","main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.22489/cinc.2016.090-500","conference":{"name":"CinC: Computing in Cardiology","end_date":"2016-09-14","start_date":"2016-09-11","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. ","lang":"eng"}],"_id":"10810","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In 2016 Computing in Cardiology Conference, 43:309–12. Computing in Cardiology, 2016. https://doi.org/10.22489/cinc.2016.090-500.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” 2016 Computing in Cardiology Conference, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:10.22489/cinc.2016.090-500.","apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., & Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In 2016 Computing in Cardiology Conference (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. https://doi.org/10.22489/cinc.2016.090-500","ieee":"P. Rubel et al., “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in 2016 Computing in Cardiology Conference, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: 2016 Computing in Cardiology Conference. Vol 43. Computing in Cardiology; 2016:309-312. doi:10.22489/cinc.2016.090-500"},"publication":"2016 Computing in Cardiology Conference","page":"309-312","date_published":"2016-03-01T00:00:00Z"},{"publication_status":"published","title":"Relevant sparse codes with variational information bottleneck","status":"public","publisher":"Neural Information Processing Systems","department":[{"_id":"GaTk"}],"intvolume":" 29","year":"2016","_id":"1082","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:03Z","date_updated":"2021-01-12T06:48:09Z","volume":29,"oa_version":"Preprint","author":[{"first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"publist_id":"6298","quality_controlled":"1","page":"1965-1973","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07332"}],"citation":{"chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 1965–1973.","mla":"Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems; 2016:1965-1973."},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain","start_date":"2016-12-05","end_date":"2016-12-10"},"date_published":"2016-12-01T00:00:00Z","scopus_import":1,"day":"01","month":"12"},{"issue":"3","publist_id":"6297","abstract":[{"lang":"eng","text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. "}],"type":"journal_article","volume":27,"oa_version":"None","date_updated":"2021-01-12T06:48:09Z","date_created":"2018-12-11T11:50:03Z","author":[{"last_name":"Booker","first_name":"Sam","full_name":"Booker, Sam"},{"full_name":"Althof, Daniel","first_name":"Daniel","last_name":"Althof"},{"full_name":"Gross, Anna","last_name":"Gross","first_name":"Anna"},{"full_name":"Loreth, Desiree","last_name":"Loreth","first_name":"Desiree"},{"full_name":"Müller, Johanna","first_name":"Johanna","last_name":"Müller"},{"full_name":"Unger, Andreas","first_name":"Andreas","last_name":"Unger"},{"full_name":"Fakler, Bernd","first_name":"Bernd","last_name":"Fakler"},{"full_name":"Varro, Andrea","first_name":"Andrea","last_name":"Varro"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"}],"department":[{"_id":"RySh"}],"publisher":"Oxford University Press","intvolume":" 27","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","status":"public","publication_status":"published","_id":"1083","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","month":"04","day":"12","language":[{"iso":"eng"}],"doi":"10.1093/cercor/bhw090","date_published":"2016-04-12T00:00:00Z","page":"2318 - 2334","quality_controlled":"1","citation":{"ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090","ieee":"S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhw090","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090."},"publication":"Cerebral Cortex"},{"date_published":"2016-08-01T00:00:00Z","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.24.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.24","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland, 2016, vol. 58.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.24","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 24."},"has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"795","oa_version":"Published Version","file":[{"file_size":564560,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","date_updated":"2018-12-12T10:17:31Z","date_created":"2018-12-12T10:17:31Z","relation":"main_file","file_id":"5286"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1090","intvolume":" 58","title":"Nested weighted limit-average automata of bounded width","ddc":["004"],"status":"public","abstract":[{"lang":"eng","text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness."}],"type":"conference","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.MFCS.2016.24","conference":{"location":"Krakow; Poland","start_date":"2016-08-22","end_date":"2016-08-26","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"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,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","month":"08","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"volume":58,"date_updated":"2021-01-12T06:48:12Z","date_created":"2018-12-11T11:50:05Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","year":"2016","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","publist_id":"6286","ec_funded":1,"file_date_updated":"2018-12-12T10:17:31Z","article_number":"24"},{"date_published":"2016-08-01T00:00:00Z","publication":"Leibniz International Proceedings in Informatics","citation":{"apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","ieee":"A. Haas et al., “Local linearizability for concurrent container-type data structures,” in Leibniz International Proceedings in Informatics, Quebec City; Canada, 2016, vol. 59.","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: Leibniz International Proceedings in Informatics. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” Leibniz International Proceedings in Informatics, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6."},"day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"793","oa_version":"Published Version","file":[{"file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","access_level":"open_access","content_type":"application/pdf","file_size":589747,"creator":"system","relation":"main_file","file_id":"4795","date_updated":"2018-12-12T10:10:10Z","date_created":"2018-12-12T10:10:10Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1095","ddc":["004"],"status":"public","title":"Local linearizability for concurrent container-type data structures","intvolume":" 59","abstract":[{"text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. ","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"conference":{"name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","location":"Quebec City; Canada","end_date":"2016-08-26"},"doi":"10.4230/LIPIcs.CONCUR.2016.6","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,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"08","author":[{"first_name":"Andreas","last_name":"Haas","full_name":"Haas, Andreas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Holzer, Andreas","first_name":"Andreas","last_name":"Holzer"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"first_name":"Michael","last_name":"Lippautz","full_name":"Lippautz, Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"full_name":"Sezgin, Ali","first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"date_created":"2018-12-11T11:50:07Z","date_updated":"2021-01-12T06:48:14Z","volume":59,"year":"2016","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:10:10Z","publist_id":"6280","ec_funded":1,"article_number":"6"},{"oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":33114420,"file_name":"IST-2017-759-v1+1_copter.pdf","access_level":"open_access","date_updated":"2018-12-12T10:17:42Z","date_created":"2018-12-12T10:17:42Z","file_id":"5298","relation":"main_file"}],"pubrep_id":"759","ddc":["006"],"status":"public","title":"Computational multicopter design","intvolume":" 35","_id":"1097","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"issue":"6","alternative_title":["ACM Transactions on Graphics"],"type":"conference","date_published":"2016-11-01T00:00:00Z","citation":{"ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427."},"day":"01","has_accepted_license":"1","scopus_import":1,"date_updated":"2021-01-12T06:48:15Z","date_created":"2018-12-11T11:50:07Z","volume":35,"author":[{"last_name":"Du","first_name":"Tao","full_name":"Du, Tao"},{"full_name":"Schulz, Adriana","last_name":"Schulz","first_name":"Adriana"},{"first_name":"Bo","last_name":"Zhu","full_name":"Zhu, Bo"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","year":"2016","file_date_updated":"2018-12-12T10:17:42Z","ec_funded":1,"publist_id":"6278","article_number":"227","language":[{"iso":"eng"}],"conference":{"location":"Macao, China","start_date":"2016-12-05","end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"doi":"10.1145/2980179.2982427","quality_controlled":"1","project":[{"name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599"}],"oa":1,"month":"11"},{"author":[{"full_name":"Pentina, Anastasia","first_name":"Anastasia","last_name":"Pentina","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Urner, Ruth","first_name":"Ruth","last_name":"Urner"}],"date_created":"2018-12-11T11:50:08Z","date_updated":"2021-01-12T06:48:15Z","volume":29,"year":"2016","acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","publication_status":"published","publisher":"Neural Information Processing Systems","department":[{"_id":"ChLa"}],"file_date_updated":"2018-12-12T10:12:43Z","ec_funded":1,"publist_id":"6277","conference":{"start_date":"2016-12-05","location":"Barcelona, Spain","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"month":"12","pubrep_id":"775","file":[{"creator":"system","content_type":"application/pdf","file_size":237111,"file_name":"IST-2017-775-v1+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:42Z","date_updated":"2018-12-12T10:12:42Z","file_id":"4961","relation":"main_file"},{"file_name":"IST-2017-775-v1+2_supplementary.pdf","access_level":"open_access","creator":"system","file_size":185818,"content_type":"application/pdf","file_id":"4962","relation":"main_file","date_created":"2018-12-12T10:12:43Z","date_updated":"2018-12-12T10:12:43Z"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1098","title":"Lifelong learning with weighted majority votes","ddc":["006"],"status":"public","intvolume":" 29","abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"type":"conference","alternative_title":["Advances in Neural Information Processing Systems"],"date_published":"2016-12-01T00:00:00Z","citation":{"chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","mla":"Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority Votes. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","apa":"Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems; 2016:3619-3627."},"page":"3619-3627","day":"01","has_accepted_license":"1","scopus_import":1},{"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"mla":"Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","apa":"Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6."},"date_published":"2016-11-01T00:00:00Z","type":"conference","alternative_title":["ACM Transactions on Graphics"],"abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"issue":"6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1099","title":"FlexMolds: Automatic design of flexible shells for molding","ddc":["000","005"],"status":"public","intvolume":" 35","pubrep_id":"760","oa_version":"Submitted Version","file":[{"file_name":"IST-2017-760-v1+1_flexmolds.pdf","access_level":"open_access","file_size":11122029,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4918","date_updated":"2018-12-12T10:12:01Z","date_created":"2018-12-12T10:12:01Z"}],"month":"11","oa":1,"quality_controlled":"1","project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020"}],"conference":{"end_date":"2016-12-08","location":"Macao, China","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"doi":"10.1145/2980179.2982397","language":[{"iso":"eng"}],"article_number":"223","file_date_updated":"2018-12-12T10:12:01Z","publist_id":"6276","ec_funded":1,"acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford 3D Scanning Repository. The bimba, fertility and elephant models are courtesy of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement\r\nNo. 645599.","year":"2016","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"}],"date_updated":"2021-01-12T06:48:16Z","date_created":"2018-12-11T11:50:08Z","volume":35},{"ec_funded":1,"publist_id":"6273","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"date_updated":"2021-01-12T06:48:18Z","date_created":"2018-12-11T11:50:09Z","volume":"2016-September","year":"2016","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"BMVA Press","month":"09","conference":{"name":"BMVC: British Machine Vision Conference","start_date":"2016-09-19","location":"York, United Kingdom","end_date":"2016-09-22"},"doi":"10.5244/C.30.92","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation.","lang":"eng"}],"type":"conference","oa_version":"Published Version","_id":"1102","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Improving weakly-supervised object localization by micro-annotation","day":"01","scopus_import":1,"date_published":"2016-09-01T00:00:00Z","publication":"Proceedings of the British Machine Vision Conference 2016","citation":{"ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: Proceedings of the British Machine Vision Conference 2016. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:10.5244/C.30.92","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in Proceedings of the British Machine Vision Conference 2016, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","apa":"Kolesnikov, A., & Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In Proceedings of the British Machine Vision Conference 2016 (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. https://doi.org/10.5244/C.30.92","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” Proceedings of the British Machine Vision Conference 2016, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:10.5244/C.30.92.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In Proceedings of the British Machine Vision Conference 2016, 2016–September:92.1-92.12. BMVA Press, 2016. https://doi.org/10.5244/C.30.92."},"page":"92.1-92.12"},{"article_number":"7797741","type":"conference","abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"ec_funded":1,"publist_id":"6272","_id":"1103","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","publication_status":"published","status":"public","title":"Parallel reachability analysis for hybrid systems","department":[{"_id":"ToHe"}],"publisher":"IEEE","author":[{"full_name":"Gurung, Amit","first_name":"Amit","last_name":"Gurung"},{"full_name":"Deka, Arup","first_name":"Arup","last_name":"Deka"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"}],"date_updated":"2021-01-12T06:48:18Z","date_created":"2018-12-11T11:50:09Z","oa_version":"Preprint","scopus_import":1,"day":"27","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"oa":1,"citation":{"ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:10.1109/MEMCOD.2016.7797741","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. https://doi.org/10.1109/MEMCOD.2016.7797741","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: International Conference on Formal Methods and Models for System Design, 7797741.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. https://doi.org/10.1109/MEMCOD.2016.7797741."},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"conference":{"end_date":"2016-11-20","start_date":"2016-11-18","location":"Kanpur, India ","name":"MEMOCODE: International Conference on Formal Methods and Models for System Design"},"doi":"10.1109/MEMCOD.2016.7797741","date_published":"2016-12-27T00:00:00Z","language":[{"iso":"eng"}]},{"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","status":"public","intvolume":" 29","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1105","oa_version":"None","alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"page":"3610-3618","citation":{"apa":"Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18."},"date_published":"2016-12-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Neural Information Processing Systems","year":"2016","acknowledgement":"We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","date_updated":"2021-01-12T06:48:19Z","date_created":"2018-12-11T11:50:10Z","volume":29,"author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"}],"publist_id":"6265","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","location":"Barcelona; Spain","start_date":"2016-12-05"},"month":"12"},{"author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"full_name":"Collodo, Michele","first_name":"Michele","last_name":"Collodo"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"full_name":"Schunk, Georg","last_name":"Schunk","first_name":"Georg"},{"last_name":"Strekalov","first_name":"Dimitry","full_name":"Strekalov, Dimitry"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"related_material":{"link":[{"url":"http://ieeexplore.ieee.org/document/7788479/","relation":"other"}]},"date_created":"2018-12-11T11:50:14Z","date_updated":"2022-09-06T07:23:25Z","oa_version":"Preprint","_id":"1115","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","publisher":"IEEE","department":[{"_id":"JoFi"}],"abstract":[{"text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth.","lang":"eng"}],"publist_id":"6251","article_number":"7788479","type":"conference","conference":{"name":"CLEO: Conference on Lasers and Electro Optics","end_date":"2016-06-10","location":"San Jose, CA, USA","start_date":"2016-06-05"},"doi":"10.1364/CLEO_SI.2016.SF2G.3","date_published":"2016-12-16T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07261"}],"citation":{"mla":"Rueda, Alfredo, et al. Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator. 7788479, IEEE, 2016, doi:10.1364/CLEO_SI.2016.SF2G.3.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:10.1364/CLEO_SI.2016.SF2G.3","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3","ieee":"A. Rueda et al., “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016."},"oa":1,"quality_controlled":"1","day":"16","month":"12","article_processing_charge":"No","scopus_import":"1"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","citation":{"ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: Proceedings of the 13th International Conference on Embedded Software . ACM; 2016. doi:10.1145/2968478.2968499","ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in Proceedings of the 13th International Conference on Embedded Software , Pittsburgh, PA, USA, 2016.","apa":"Avni, G., Guha, S., & Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In Proceedings of the 13th International Conference on Embedded Software . Pittsburgh, PA, USA: ACM. https://doi.org/10.1145/2968478.2968499","ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26.","short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016.","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” Proceedings of the 13th International Conference on Embedded Software , 26, ACM, 2016, doi:10.1145/2968478.2968499.","chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In Proceedings of the 13th International Conference on Embedded Software . ACM, 2016. https://doi.org/10.1145/2968478.2968499."},"publication":"Proceedings of the 13th International Conference on Embedded Software ","abstract":[{"text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM.","lang":"eng"}],"type":"conference","file":[{"file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","access_level":"open_access","content_type":"application/pdf","file_size":279240,"creator":"system","relation":"main_file","file_id":"4755","date_updated":"2018-12-12T10:09:31Z","date_created":"2018-12-12T10:09:31Z"}],"oa_version":"Submitted Version","pubrep_id":"644","status":"public","title":"Synthesizing time triggered schedules for switched networks with faulty links","ddc":["000"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1135","month":"10","language":[{"iso":"eng"}],"doi":"10.1145/2968478.2968499","conference":{"start_date":"2016-10-01","location":"Pittsburgh, PA, USA","end_date":"2016-10-07","name":"EMSOFT: Embedded Software "},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","oa":1,"publist_id":"6223","ec_funded":1,"file_date_updated":"2018-12-12T10:09:31Z","article_number":"26","date_created":"2018-12-11T11:50:20Z","date_updated":"2021-01-12T06:48:33Z","author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Guillermo","last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo"}],"publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2016"},{"author":[{"last_name":"Duggirala","first_name":"Parasara","full_name":"Duggirala, Parasara"},{"full_name":"Fan, Chuchu","first_name":"Chuchu","last_name":"Fan"},{"full_name":"Potok, Matthew","first_name":"Matthew","last_name":"Potok"},{"first_name":"Bolun","last_name":"Qi","full_name":"Qi, Bolun"},{"last_name":"Mitra","first_name":"Sayan","full_name":"Mitra, Sayan"},{"full_name":"Viswanathan, Mahesh","first_name":"Mahesh","last_name":"Viswanathan"},{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"},{"full_name":"Nguyen, Luan","first_name":"Luan","last_name":"Nguyen"},{"last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"},{"full_name":"Sogokon, Andrew","first_name":"Andrew","last_name":"Sogokon"},{"full_name":"Tran, Hoang","first_name":"Hoang","last_name":"Tran"},{"first_name":"Weiming","last_name":"Xiang","full_name":"Xiang, Weiming"}],"date_updated":"2021-01-12T06:48:32Z","date_created":"2018-12-11T11:50:20Z","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1134","year":"2016","publication_status":"published","title":"Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP","status":"public","department":[{"_id":"ToHe"}],"publisher":"IEEE","abstract":[{"lang":"eng","text":"Hybrid systems have both continuous and discrete dynamics and are useful for modeling a variety of control systems, from air traffic control protocols to robotic maneuvers and beyond. Recently, numerous powerful and scalable tools for analyzing hybrid systems have emerged. Several of these tools implement automated formal methods for mathematically proving a system meets a specification. This tutorial session will present three recent hybrid systems tools: C2E2, HyST, and TuLiP. C2E2 is a simulated-based verification tool for hybrid systems, and uses validated numerical solvers and bloating of simulation traces to verify systems meet specifications. HyST is a hybrid systems model transformation and translation tool, and uses a canonical intermediate representation to support most of the recent verification tools, as well as automated sound abstractions that simplify verification of a given hybrid system. TuLiP is a controller synthesis tool for hybrid systems, where given a temporal logic specification to be satisfied for a system (plant) model, TuLiP will find a controller that meets a given specification. © 2016 IEEE."}],"publist_id":"6224","article_number":"7587948","type":"conference","conference":{"name":"CCA: Control Applications ","location":"Buenos Aires, Argentina ","start_date":"2016-09-19","end_date":"2016-09-22"},"date_published":"2016-10-10T00:00:00Z","doi":"10.1109/CCA.2016.7587948","language":[{"iso":"eng"}],"publication":"2016 IEEE Conference on Control Applications","citation":{"chicago":"Duggirala, Parasara, Chuchu Fan, Matthew Potok, Bolun Qi, Sayan Mitra, Mahesh Viswanathan, Stanley Bak, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” In 2016 IEEE Conference on Control Applications. IEEE, 2016. https://doi.org/10.1109/CCA.2016.7587948.","short":"P. Duggirala, C. Fan, M. Potok, B. Qi, S. Mitra, M. Viswanathan, S. Bak, S. Bogomolov, T. Johnson, L. Nguyen, C. Schilling, A. Sogokon, H. Tran, W. Xiang, in:, 2016 IEEE Conference on Control Applications, IEEE, 2016.","mla":"Duggirala, Parasara, et al. “Tutorial: Software Tools for Hybrid Systems Verification Transformation and Synthesis C2E2 HyST and TuLiP.” 2016 IEEE Conference on Control Applications, 7587948, IEEE, 2016, doi:10.1109/CCA.2016.7587948.","apa":"Duggirala, P., Fan, C., Potok, M., Qi, B., Mitra, S., Viswanathan, M., … Xiang, W. (2016). Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In 2016 IEEE Conference on Control Applications. Buenos Aires, Argentina : IEEE. https://doi.org/10.1109/CCA.2016.7587948","ieee":"P. Duggirala et al., “Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP,” in 2016 IEEE Conference on Control Applications, Buenos Aires, Argentina , 2016.","ista":"Duggirala P, Fan C, Potok M, Qi B, Mitra S, Viswanathan M, Bak S, Bogomolov S, Johnson T, Nguyen L, Schilling C, Sogokon A, Tran H, Xiang W. 2016. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. 2016 IEEE Conference on Control Applications. CCA: Control Applications , 7587948.","ama":"Duggirala P, Fan C, Potok M, et al. Tutorial: Software tools for hybrid systems verification transformation and synthesis C2E2 HyST and TuLiP. In: 2016 IEEE Conference on Control Applications. IEEE; 2016. doi:10.1109/CCA.2016.7587948"},"quality_controlled":"1","month":"10","day":"10","scopus_import":1},{"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2016-10-10T00:00:00Z","publication":"Proceedings of the 9th International Conference on Motion in Games ","citation":{"short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016.","mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” Proceedings of the 9th International Conference on Motion in Games , 2994261, ACM, 2016, doi:10.1145/2994258.2994261.","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In Proceedings of the 9th International Conference on Motion in Games . ACM, 2016. https://doi.org/10.1145/2994258.2994261.","ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: Proceedings of the 9th International Conference on Motion in Games . ACM; 2016. doi:10.1145/2994258.2994261","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., & Cani, M. (2016). Space-time sculpting of liquid animation. In Proceedings of the 9th International Conference on Motion in Games . San Francisco, CA, USA: ACM. https://doi.org/10.1145/2994258.2994261","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in Proceedings of the 9th International Conference on Motion in Games , San Francisco, CA, USA, 2016.","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261."},"abstract":[{"text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s).","lang":"eng"}],"type":"conference","oa_version":"Submitted Version","status":"public","ddc":["004"],"title":"Space-time sculpting of liquid animation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1136","month":"10","language":[{"iso":"eng"}],"conference":{"name":"MIG: Motion in Games","start_date":"2016-10-10","location":"San Francisco, CA, USA","end_date":"2016-10-12"},"doi":"10.1145/2994258.2994261","quality_controlled":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01367181"}],"oa":1,"publist_id":"6222","ec_funded":1,"article_number":"2994261","date_updated":"2023-02-21T09:49:49Z","date_created":"2018-12-11T11:50:20Z","author":[{"full_name":"Manteaux, Pierre","first_name":"Pierre","last_name":"Manteaux"},{"last_name":"Vimont","first_name":"Ulysse","full_name":"Vimont, Ulysse"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rohmer, Damien","last_name":"Rohmer","first_name":"Damien"},{"full_name":"Cani, Marie","last_name":"Cani","first_name":"Marie"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","year":"2016"},{"scopus_import":1,"day":"01","article_processing_charge":"No","article_type":"original","page":"1352 - 1360","publication":"Nature Immunology","citation":{"ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","ieee":"E. Salzer et al., “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” Nature Immunology, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3575","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 2016;17(12):1352-1360. doi:10.1038/ni.3575","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” Nature Immunology. Nature Publishing Group, 2016. https://doi.org/10.1038/ni.3575.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” Nature Immunology, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:10.1038/ni.3575.","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360."},"date_published":"2016-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes."}],"issue":"12","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","status":"public","intvolume":" 17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1137","oa_version":"Submitted Version","month":"12","quality_controlled":"1","external_id":{"pmid":["27776107"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263"}],"language":[{"iso":"eng"}],"doi":"10.1038/ni.3575","publist_id":"6221","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","year":"2016","pmid":1,"date_created":"2018-12-11T11:50:21Z","date_updated":"2021-01-12T06:48:33Z","volume":17,"author":[{"full_name":"Salzer, Elisabeth","last_name":"Salzer","first_name":"Elisabeth"},{"full_name":"Çaǧdaş, Deniz","last_name":"Çaǧdaş","first_name":"Deniz"},{"full_name":"Hons, Miroslav","last_name":"Hons","first_name":"Miroslav","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emily","last_name":"Mace","full_name":"Mace, Emily"},{"full_name":"Garncarz, Wojciech","first_name":"Wojciech","last_name":"Garncarz"},{"first_name":"Oezlem","last_name":"Petronczki","full_name":"Petronczki, Oezlem"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"first_name":"Laurène","last_name":"Pfajfer","full_name":"Pfajfer, Laurène"},{"first_name":"Ivan","last_name":"Bilic","full_name":"Bilic, Ivan"},{"full_name":"Ban, Sol","last_name":"Ban","first_name":"Sol"},{"first_name":"Katharina","last_name":"Willmann","full_name":"Willmann, Katharina"},{"first_name":"Malini","last_name":"Mukherjee","full_name":"Mukherjee, Malini"},{"first_name":"Verena","last_name":"Supper","full_name":"Supper, Verena"},{"full_name":"Hsu, Hsiangting","first_name":"Hsiangting","last_name":"Hsu"},{"full_name":"Banerjee, Pinaki","last_name":"Banerjee","first_name":"Pinaki"},{"full_name":"Sinha, Papiya","last_name":"Sinha","first_name":"Papiya"},{"last_name":"Mcclanahan","first_name":"Fabienne","full_name":"Mcclanahan, Fabienne"},{"first_name":"Gerhard","last_name":"Zlabinger","full_name":"Zlabinger, Gerhard"},{"last_name":"Pickl","first_name":"Winfried","full_name":"Pickl, Winfried"},{"first_name":"John","last_name":"Gribben","full_name":"Gribben, John"},{"full_name":"Stockinger, Hannes","last_name":"Stockinger","first_name":"Hannes"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"full_name":"Huppa, Johannes","first_name":"Johannes","last_name":"Huppa"},{"full_name":"Dupré, Loï̈C","last_name":"Dupré","first_name":"Loï̈C"},{"full_name":"Sanal, Özden","first_name":"Özden","last_name":"Sanal"},{"first_name":"Ulrich","last_name":"Jäger","full_name":"Jäger, Ulrich"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Tezcan, Ilhan","first_name":"Ilhan","last_name":"Tezcan"},{"full_name":"Orange, Jordan","first_name":"Jordan","last_name":"Orange"},{"full_name":"Boztug, Kaan","last_name":"Boztug","first_name":"Kaan"}]},{"month":"07","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1604.06764"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"language":[{"iso":"eng"}],"doi":"10.1145/2933575.2933588","conference":{"start_date":"2016-07-05","location":"New York, NY, USA","end_date":"2016-07-08","name":"LICS: Logic in Computer Science"},"ec_funded":1,"publist_id":"6220","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2016","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","date_updated":"2021-01-12T06:48:34Z","date_created":"2018-12-11T11:50:21Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"day":"05","page":"76 - 85","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in Proceedings of the 31st Annual ACM/IEEE Symposium, New York, NY, USA, 2016, pp. 76–85.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative automata under probabilistic semantics. In Proceedings of the 31st Annual ACM/IEEE Symposium (pp. 76–85). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2933588","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: Proceedings of the 31st Annual ACM/IEEE Symposium. IEEE; 2016:76-85. doi:10.1145/2933575.2933588","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In Proceedings of the 31st Annual ACM/IEEE Symposium, 76–85. IEEE, 2016. https://doi.org/10.1145/2933575.2933588.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85, doi:10.1145/2933575.2933588."},"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","date_published":"2016-07-05T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM."}],"status":"public","title":"Quantitative automata under probabilistic semantics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1138","oa_version":"Preprint"},{"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","external_id":{"arxiv":["1602.02670"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1145/2933575.2935304","conference":{"name":"LICS: Logic in Computer Science","end_date":"2016-07-08","start_date":"2016-07-05","location":"New York, NY, USA"},"month":"07","department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","year":"2016","date_updated":"2022-09-09T11:46:17Z","date_created":"2018-12-11T11:50:22Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dvoák, Wolfgang","last_name":"Dvoák","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"publist_id":"6219","page":"197 - 206","citation":{"short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206, doi:10.1145/2933575.2935304.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, 197–206. IEEE, 2016. https://doi.org/10.1145/2933575.2935304.","ama":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2016:197-206. doi:10.1145/2933575.2935304","ieee":"K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, New York, NY, USA, 2016, pp. 197–206.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., & Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 197–206). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2935304","ista":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206."},"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","date_published":"2016-07-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"05","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1140","oa_version":"Preprint","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"type":"conference","abstract":[{"lang":"eng","text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM."}]},{"doi":"10.1038/ni.3590","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"quality_controlled":"1","month":"12","author":[{"full_name":"Martins, Rui","last_name":"Martins","first_name":"Rui"},{"full_name":"Maier, Julia","last_name":"Maier","first_name":"Julia"},{"last_name":"Gorki","first_name":"Anna","full_name":"Gorki, Anna"},{"full_name":"Huber, Kilian","first_name":"Kilian","last_name":"Huber"},{"full_name":"Sharif, Omar","last_name":"Sharif","first_name":"Omar"},{"last_name":"Starkl","first_name":"Philipp","full_name":"Starkl, Philipp"},{"first_name":"Simona","last_name":"Saluzzo","full_name":"Saluzzo, Simona"},{"full_name":"Quattrone, Federica","last_name":"Quattrone","first_name":"Federica"},{"full_name":"Gawish, Riem","first_name":"Riem","last_name":"Gawish"},{"full_name":"Lakovits, Karin","last_name":"Lakovits","first_name":"Karin"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael"},{"full_name":"Radic Sarikas, Branka","first_name":"Branka","last_name":"Radic Sarikas"},{"full_name":"Lardeau, Charles","last_name":"Lardeau","first_name":"Charles"},{"full_name":"Hladik, Anastasiya","first_name":"Anastasiya","last_name":"Hladik"},{"last_name":"Korosec","first_name":"Ana","full_name":"Korosec, Ana"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle","last_name":"Duggan","full_name":"Duggan, Michelle"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"full_name":"Esterbauer, Harald","last_name":"Esterbauer","first_name":"Harald"},{"full_name":"Colinge, Jacques","first_name":"Jacques","last_name":"Colinge"},{"full_name":"Eisenbarth, Stephanie","last_name":"Eisenbarth","first_name":"Stephanie"},{"first_name":"Thomas","last_name":"Decker","full_name":"Decker, Thomas"},{"full_name":"Bennett, Keiryn","first_name":"Keiryn","last_name":"Bennett"},{"full_name":"Kubicek, Stefan","last_name":"Kubicek","first_name":"Stefan"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Superti Furga, Giulio","last_name":"Superti Furga","first_name":"Giulio"},{"full_name":"Knapp, Sylvia","last_name":"Knapp","first_name":"Sylvia"}],"volume":17,"date_updated":"2021-01-12T06:48:36Z","date_created":"2018-12-11T11:50:22Z","year":"2016","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"publisher":"Nature Publishing Group","publication_status":"published","publist_id":"6216","date_published":"2016-12-01T00:00:00Z","citation":{"apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/ni.3590","ieee":"R. Martins et al., “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” Nature Immunology, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 2016;17(12):1361-1372. doi:10.1038/ni.3590","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” Nature Immunology. Nature Publishing Group, 2016. https://doi.org/10.1038/ni.3590.","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” Nature Immunology, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:10.1038/ni.3590."},"publication":"Nature Immunology","page":"1361 - 1372","day":"01","scopus_import":1,"oa_version":"Submitted Version","_id":"1142","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 17","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","status":"public","issue":"12","abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"type":"journal_article"},{"date_created":"2018-12-11T11:50:22Z","date_updated":"2021-01-12T06:48:35Z","volume":17,"oa_version":"None","author":[{"last_name":"Łazarz","first_name":"Radosław","full_name":"Łazarz, Radosław"},{"last_name":"Idzik","first_name":"Michał","full_name":"Idzik, Michał"},{"first_name":"Konrad","last_name":"Gądek","full_name":"Gądek, Konrad"},{"full_name":"Gajda-Zagorska, Ewa P","last_name":"Gajda-Zagorska","first_name":"Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87"}],"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","publication_status":"published","status":"public","publisher":"Elsevier","intvolume":" 17","department":[{"_id":"ChWo"}],"acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","_id":"1141","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","abstract":[{"text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.","lang":"eng"}],"publist_id":"6217","issue":"1","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2016-11-01T00:00:00Z","doi":"10.1016/j.jocs.2016.03.004","quality_controlled":"1","page":"249 - 260","publication":"Journal of Computational Science","citation":{"short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” Journal of Computational Science, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:10.1016/j.jocs.2016.03.004.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” Journal of Computational Science. Elsevier, 2016. https://doi.org/10.1016/j.jocs.2016.03.004.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 2016;17(1):249-260. doi:10.1016/j.jocs.2016.03.004","apa":"Łazarz, R., Idzik, M., Gądek, K., & Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.03.004","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” Journal of Computational Science, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260."},"day":"01","month":"11","scopus_import":1},{"author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"date_created":"2018-12-11T11:50:23Z","date_updated":"2021-01-12T06:48:36Z","volume":9,"year":"2016","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","ec_funded":1,"publist_id":"6215","doi":"10.2140/apde.2016.9.459","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"03","oa_version":"Preprint","_id":"1143","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","status":"public","intvolume":" 9","abstract":[{"lang":"eng","text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present."}],"issue":"2","type":"journal_article","date_published":"2016-03-24T00:00:00Z","publication":"Analysis and PDE","citation":{"ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 2016;9(2):459-485. doi:10.2140/apde.2016.9.459","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” Analysis and PDE, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","apa":"Nam, P., Rougerie, N., & Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/apde.2016.9.459","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:10.2140/apde.2016.9.459.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” Analysis and PDE. Mathematical Sciences Publishers, 2016. https://doi.org/10.2140/apde.2016.9.459."},"page":"459 - 485","day":"24","scopus_import":1},{"month":"11","doi":"10.1016/j.molp.2016.08.010","language":[{"iso":"eng"}],"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","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2018-12-12T10:13:22Z","ec_funded":1,"publist_id":"6213","author":[{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"date_updated":"2021-01-12T06:48:37Z","date_created":"2018-12-11T11:50:23Z","volume":9,"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","year":"2016","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","day":"07","has_accepted_license":"1","scopus_import":1,"date_published":"2016-11-07T00:00:00Z","publication":"Molecular Plant","citation":{"chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., & Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010"},"page":"1504 - 1519","abstract":[{"text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors","lang":"eng"}],"issue":"11","type":"journal_article","pubrep_id":"746","file":[{"file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5005876,"creator":"system","relation":"main_file","file_id":"5004","date_created":"2018-12-12T10:13:22Z","date_updated":"2018-12-12T10:13:22Z"}],"oa_version":"Published Version","_id":"1145","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["581"],"status":"public","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","intvolume":" 9"},{"file":[{"file_name":"IST-2017-745-v1+1_srep35955.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1587544,"file_id":"4752","relation":"main_file","date_created":"2018-12-12T10:09:28Z","date_updated":"2018-12-12T10:09:28Z"}],"oa_version":"Published Version","pubrep_id":"745","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","ddc":["581"],"status":"public","intvolume":" 6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1147","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"type":"journal_article","date_published":"2016-11-08T00:00:00Z","publication":"Scientific Reports","citation":{"chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature Publishing Group, 2016, doi:10.1038/srep35955.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., & Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep35955","ieee":"J. Balla et al., “Auxin flow mediated competition between axillary buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 2016;6. doi:10.1038/srep35955"},"day":"08","has_accepted_license":"1","scopus_import":1,"date_updated":"2021-01-12T06:48:38Z","date_created":"2018-12-11T11:50:24Z","volume":6,"author":[{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"first_name":"Zuzana","last_name":"Medved'Ová","full_name":"Medved'Ová, Zuzana"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"first_name":"Natálie","last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Reinöhl, Vilém","last_name":"Reinöhl","first_name":"Vilém"},{"full_name":"Procházka, Stanislav","first_name":"Stanislav","last_name":"Procházka"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"year":"2016","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","file_date_updated":"2018-12-12T10:09:28Z","publist_id":"6211","article_number":"35955","language":[{"iso":"eng"}],"doi":"10.1038/srep35955","quality_controlled":"1","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"},"month":"11"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.apnum.2016.04.005","date_published":"2016-09-01T00:00:00Z","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"page":"34 - 47","publication":"Applied Numerical Mathematics","citation":{"ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., & Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2016.04.005","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” Applied Numerical Mathematics, vol. 107. Elsevier, pp. 34–47, 2016.","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 2016;107:34-47. doi:10.1016/j.apnum.2016.04.005","chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” Applied Numerical Mathematics. Elsevier, 2016. https://doi.org/10.1016/j.apnum.2016.04.005.","mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” Applied Numerical Mathematics, vol. 107, Elsevier, 2016, pp. 34–47, doi:10.1016/j.apnum.2016.04.005.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47."},"day":"01","month":"09","scopus_import":1,"date_updated":"2021-01-12T06:48:38Z","date_created":"2018-12-11T11:50:25Z","oa_version":"None","volume":107,"author":[{"first_name":"Tomoyuki","last_name":"Miyaji","full_name":"Miyaji, Tomoyuki"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"},{"full_name":"Gameiro, Marcio","last_name":"Gameiro","first_name":"Marcio"},{"first_name":"Hiroshi","last_name":"Kokubu","full_name":"Kokubu, Hiroshi"},{"first_name":"Konstantin","last_name":"Mischaikow","full_name":"Mischaikow, Konstantin"}],"status":"public","title":"A study of rigorous ODE integrators for multi scale set oriented computations","publication_status":"published","publisher":"Elsevier","intvolume":" 107","department":[{"_id":"HeEd"}],"_id":"1149","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","year":"2016","abstract":[{"lang":"eng","text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved."}],"ec_funded":1,"publist_id":"6209","type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc."}],"publist_id":"6208","issue":"5","status":"public","publication_status":"published","title":"A Radical Break Restraining Neutrophil Migration","publisher":"Cell Press","department":[{"_id":"MiSi"}],"intvolume":" 38","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1150","year":"2016","date_created":"2018-12-11T11:50:25Z","date_updated":"2021-01-12T06:48:39Z","oa_version":"None","volume":38,"author":[{"full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"scopus_import":1,"month":"09","day":"12","quality_controlled":"1","page":"448 - 450","publication":"Developmental Cell","citation":{"short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:10.1016/j.devcel.2016.08.017.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.08.017.","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 2016;38(5):448-450. doi:10.1016/j.devcel.2016.08.017","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” Developmental Cell, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","apa":"Renkawitz, J., & Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.08.017","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450."},"language":[{"iso":"eng"}],"date_published":"2016-09-12T00:00:00Z","doi":"10.1016/j.devcel.2016.08.017"},{"day":"15","has_accepted_license":"1","scopus_import":1,"date_published":"2016-10-15T00:00:00Z","publication":"Genes and Development","citation":{"ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","ieee":"S. Simonini et al., “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 2016;30(20):2286-2296. doi:10.1101/gad.285361.116","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.285361.116.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296."},"page":"2286 - 2296","abstract":[{"lang":"eng","text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al."}],"issue":"20","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2016_GeneDev_Simonini.pdf","file_size":1419263,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5882","success":1,"date_updated":"2019-01-25T09:32:55Z","date_created":"2019-01-25T09:32:55Z"}],"_id":"1151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","ddc":["570"],"status":"public","intvolume":" 30","month":"10","doi":"10.1101/gad.285361.116","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"},"external_id":{"pmid":["27898393"]},"oa":1,"quality_controlled":"1","file_date_updated":"2019-01-25T09:32:55Z","publist_id":"6207","author":[{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"full_name":"Deb, Joyita","last_name":"Deb","first_name":"Joyita"},{"last_name":"Moubayidin","first_name":"Laila","full_name":"Moubayidin, Laila"},{"last_name":"Stephenson","first_name":"Pauline","full_name":"Stephenson, Pauline"},{"full_name":"Valluru, Manoj","first_name":"Manoj","last_name":"Valluru"},{"full_name":"Freire Rios, Alejandra","last_name":"Freire Rios","first_name":"Alejandra"},{"full_name":"Sorefan, Karim","first_name":"Karim","last_name":"Sorefan"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Östergaard, Lars","first_name":"Lars","last_name":"Östergaard"}],"date_updated":"2021-01-12T06:48:39Z","date_created":"2018-12-11T11:50:25Z","volume":30,"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","year":"2016","pmid":1,"publication_status":"published","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"JiFr"}]},{"oa_version":"Submitted Version","_id":"1153","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A model of differential growth guided apical hook formation in plants","intvolume":" 28","abstract":[{"text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2016-10-01T00:00:00Z","publication":"Plant Cell","citation":{"chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569"},"page":"2464 - 2477","day":"01","scopus_import":1,"author":[{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"full_name":"Gallemí, Marçal","last_name":"Gallemí","first_name":"Marçal"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"first_name":"Richard","last_name":"Smith","full_name":"Smith, Richard"},{"first_name":"Dirk","last_name":"Inze","full_name":"Inze, Dirk"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Prusinkiewicz","first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"date_created":"2018-12-11T11:50:26Z","date_updated":"2021-01-12T06:48:40Z","volume":28,"acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","year":"2016","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","ec_funded":1,"publist_id":"6205","doi":"10.1105/tpc.15.00569","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"quality_controlled":"1","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"month":"10"},{"date_published":"2016-11-07T00:00:00Z","citation":{"ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep36440","ieee":"J. Schwarz et al., “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 2016;6. doi:10.1038/srep36440","chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol. 6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016)."},"publication":"Scientific Reports","has_accepted_license":"1","day":"07","scopus_import":1,"oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:09:32Z","date_updated":"2018-12-12T10:09:32Z","file_id":"4756","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2353456,"access_level":"open_access","file_name":"IST-2017-744-v1+1_srep36440.pdf"}],"pubrep_id":"744","intvolume":" 6","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","status":"public","ddc":["579"],"_id":"1154","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/srep36440","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","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"},"month":"11","volume":6,"date_updated":"2021-01-12T06:48:41Z","date_created":"2018-12-11T11:50:27Z","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"first_name":"Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Frank, Tino","first_name":"Tino","last_name":"Frank"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"},{"full_name":"Tay, Savaş","last_name":"Tay","first_name":"Savaş"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"orcid":"0000-0001-8599-1226","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","last_name":"Mehling","first_name":"Matthias","full_name":"Mehling, Matthias"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2016","acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","publist_id":"6204","ec_funded":1,"file_date_updated":"2018-12-12T10:09:32Z","article_number":"36440"}]