[{"date_published":"2017-12-01T00:00:00Z","publication":"Nature Communications","external_id":{"isi":["000413571300004"]},"article_number":"1103","quality_controlled":"1","intvolume":"         8","month":"12","author":[{"first_name":"Elisabetta","full_name":"Aloisi, Elisabetta","last_name":"Aloisi"},{"last_name":"Le Corf","full_name":"Le Corf, Katy","first_name":"Katy"},{"first_name":"Julien","full_name":"Dupuis, Julien","last_name":"Dupuis"},{"last_name":"Zhang","first_name":"Pei","full_name":"Zhang, Pei"},{"full_name":"Ginger, Melanie","first_name":"Melanie","last_name":"Ginger"},{"first_name":"Virginie","full_name":"Labrousse, Virginie","last_name":"Labrousse"},{"last_name":"Spatuzza","first_name":"Michela","full_name":"Spatuzza, Michela"},{"first_name":"Matthias","full_name":"Georg Haberl, Matthias","last_name":"Georg Haberl"},{"full_name":"Costa, Lara","first_name":"Lara","last_name":"Costa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"},{"first_name":"Anke","full_name":"Tappe Theodor, Anke","last_name":"Tappe Theodor"},{"first_name":"Fillippo","full_name":"Drago, Fillippo","last_name":"Drago"},{"full_name":"Vincenzo Piazza, Pier","first_name":"Pier","last_name":"Vincenzo Piazza"},{"first_name":"Christophe","full_name":"Mulle, Christophe","last_name":"Mulle"},{"last_name":"Groc","first_name":"Laurent","full_name":"Groc, Laurent"},{"full_name":"Ciranna, Lucia","first_name":"Lucia","last_name":"Ciranna"},{"last_name":"Catania","first_name":"Maria","full_name":"Catania, Maria"},{"last_name":"Frick","full_name":"Frick, Andreas","first_name":"Andreas"}],"year":"2017","doi":"10.1038/s41467-017-01191-2","has_accepted_license":"1","file":[{"relation":"main_file","file_id":"5287","content_type":"application/pdf","date_updated":"2020-07-14T12:47:58Z","file_name":"IST-2017-915-v1+1_s41467-017-01191-2.pdf","date_created":"2018-12-12T10:17:32Z","creator":"system","access_level":"open_access","file_size":1841650,"checksum":"99ceee57549dc0461e3adfc037ec70a9"}],"ddc":["571"],"oa_version":"Published Version","publication_status":"published","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"},"article_processing_charge":"No","oa":1,"isi":1,"date_updated":"2023-09-27T12:27:30Z","abstract":[{"text":"Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics.","lang":"eng"}],"volume":8,"date_created":"2018-12-11T11:48:17Z","language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"publisher":"Nature Publishing Group","_id":"746","pubrep_id":"915","day":"01","citation":{"mla":"Aloisi, Elisabetta, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” <i>Nature Communications</i>, vol. 8, no. 1, 1103, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01191-2\">10.1038/s41467-017-01191-2</a>.","ista":"Aloisi E, Le Corf K, Dupuis J, Zhang P, Ginger M, Labrousse V, Spatuzza M, Georg Haberl M, Costa L, Shigemoto R, Tappe Theodor A, Drago F, Vincenzo Piazza P, Mulle C, Groc L, Ciranna L, Catania M, Frick A. 2017. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. Nature Communications. 8(1), 1103.","chicago":"Aloisi, Elisabetta, Katy Le Corf, Julien Dupuis, Pei Zhang, Melanie Ginger, Virginie Labrousse, Michela Spatuzza, et al. “Altered Surface MGluR5 Dynamics Provoke Synaptic NMDAR Dysfunction and Cognitive Defects in Fmr1 Knockout Mice.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01191-2\">https://doi.org/10.1038/s41467-017-01191-2</a>.","ieee":"E. Aloisi <i>et al.</i>, “Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Aloisi, E., Le Corf, K., Dupuis, J., Zhang, P., Ginger, M., Labrousse, V., … Frick, A. (2017). Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01191-2\">https://doi.org/10.1038/s41467-017-01191-2</a>","ama":"Aloisi E, Le Corf K, Dupuis J, et al. Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01191-2\">10.1038/s41467-017-01191-2</a>","short":"E. Aloisi, K. Le Corf, J. Dupuis, P. Zhang, M. Ginger, V. Labrousse, M. Spatuzza, M. Georg Haberl, L. Costa, R. Shigemoto, A. Tappe Theodor, F. Drago, P. Vincenzo Piazza, C. Mulle, L. Groc, L. Ciranna, M. Catania, A. Frick, Nature Communications 8 (2017)."},"publication_identifier":{"issn":["20411723"]},"title":"Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice","scopus_import":"1","status":"public","publist_id":"6921","type":"journal_article","issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:47:58Z"},{"pmid":1,"date_published":"2017-12-04T00:00:00Z","external_id":{"pmid":["28951324"],"isi":["000415966200003"]},"publication":"Neuroscience","intvolume":"       365","author":[{"full_name":"Brǎiloiu, Eugen","first_name":"Eugen","last_name":"Brǎiloiu"},{"last_name":"Mcguire","full_name":"Mcguire, Matthew","first_name":"Matthew"},{"last_name":"Shuler","first_name":"Shadaria","full_name":"Shuler, Shadaria"},{"id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu","full_name":"Deliu, Elena","first_name":"Elena","orcid":"0000-0002-7370-5293"},{"first_name":"Jeffrey","full_name":"Barr, Jeffrey","last_name":"Barr"},{"first_name":"Mary","full_name":"Abood, Mary","last_name":"Abood"},{"last_name":"Brailoiu","first_name":"Gabriela","full_name":"Brailoiu, Gabriela"}],"month":"12","quality_controlled":"1","year":"2017","doi":"10.1016/j.neuroscience.2017.09.034","publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","volume":365,"date_created":"2018-12-11T11:48:17Z","abstract":[{"text":"Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"isi":1,"article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458"}],"date_updated":"2023-09-27T12:26:59Z","_id":"747","publisher":"Elsevier","day":"04","citation":{"ista":"Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 365, 23–32.","mla":"Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” <i>Neuroscience</i>, vol. 365, Elsevier, 2017, pp. 23–32, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">10.1016/j.neuroscience.2017.09.034</a>.","chicago":"Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” <i>Neuroscience</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">https://doi.org/10.1016/j.neuroscience.2017.09.034</a>.","ieee":"E. Brǎiloiu <i>et al.</i>, “Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus,” <i>Neuroscience</i>, vol. 365. Elsevier, pp. 23–32, 2017.","apa":"Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., &#38; Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">https://doi.org/10.1016/j.neuroscience.2017.09.034</a>","ama":"Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. <i>Neuroscience</i>. 2017;365:23-32. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">10.1016/j.neuroscience.2017.09.034</a>","short":"E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu, Neuroscience 365 (2017) 23–32."},"department":[{"_id":"GaNo"}],"page":"23 - 32","status":"public","scopus_import":"1","publication_identifier":{"issn":["03064522"]},"title":"Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus","publist_id":"6911","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_identifier":{"issn":["22111247"]},"title":"Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses","scopus_import":"1","status":"public","page":"2082 - 2089","type":"journal_article","publist_id":"6907","acknowledged_ssus":[{"_id":"PreCl"}],"issue":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z","isi":1,"oa":1,"date_updated":"2023-09-27T12:26:04Z","abstract":[{"text":"Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission","lang":"eng"}],"date_created":"2018-12-11T11:48:18Z","volume":21,"language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"day":"21","pubrep_id":"874","_id":"749","publisher":"Cell Press","citation":{"mla":"Chen, Chong, et al. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” <i>Cell Reports</i>, vol. 21, no. 8, Cell Press, 2017, pp. 2082–89, doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.10.122\">10.1016/j.celrep.2017.10.122</a>.","ista":"Chen C, Satterfield R, Young S, Jonas PM. 2017. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. Cell Reports. 21(8), 2082–2089.","chicago":"Chen, Chong, Rachel Satterfield, Samuel Young, and Peter M Jonas. “Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2017.10.122\">https://doi.org/10.1016/j.celrep.2017.10.122</a>.","ieee":"C. Chen, R. Satterfield, S. Young, and P. M. Jonas, “Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses,” <i>Cell Reports</i>, vol. 21, no. 8. Cell Press, pp. 2082–2089, 2017.","apa":"Chen, C., Satterfield, R., Young, S., &#38; Jonas, P. M. (2017). Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2017.10.122\">https://doi.org/10.1016/j.celrep.2017.10.122</a>","ama":"Chen C, Satterfield R, Young S, Jonas PM. Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses. <i>Cell Reports</i>. 2017;21(8):2082-2089. doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.10.122\">10.1016/j.celrep.2017.10.122</a>","short":"C. Chen, R. Satterfield, S. Young, P.M. Jonas, Cell Reports 21 (2017) 2082–2089."},"year":"2017","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"4737","date_updated":"2020-07-14T12:47:59Z","date_created":"2018-12-12T10:09:14Z","file_name":"IST-2017-874-v1+1_PIIS2211124717316029.pdf","creator":"system","access_level":"open_access","checksum":"a6afa3764909bf6edafa07982d8e1cee","file_size":2759195}],"has_accepted_license":"1","doi":"10.1016/j.celrep.2017.10.122","ddc":["570","571"],"related_material":{"record":[{"id":"324","relation":"dissertation_contains","status":"public"}]},"project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"}],"oa_version":"Published Version","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"},"publication_status":"published","article_processing_charge":"No","date_published":"2017-11-21T00:00:00Z","publication":"Cell Reports","external_id":{"isi":["000416216700007"]},"quality_controlled":"1","intvolume":"        21","month":"11","author":[{"full_name":"Chen, Chong","first_name":"Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rachel","full_name":"Satterfield, Rachel","last_name":"Satterfield"},{"full_name":"Young, Samuel","first_name":"Samuel","last_name":"Young"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}]},{"day":"01","publisher":"IEEE","_id":"750","month":"12","author":[{"id":"49BC895A-F248-11E8-B48F-1D18A9856A87","last_name":"Pielorz","full_name":"Pielorz, Jasmin","first_name":"Jasmin"},{"first_name":"Matthias","full_name":"Prandtstetter, Matthias","last_name":"Prandtstetter"},{"last_name":"Straub","first_name":"Markus","full_name":"Straub, Markus"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"citation":{"short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","apa":"Pielorz, J., Prandtstetter, M., Straub, M., &#38; Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In <i>2017 IEEE International Conference on Big Data</i> (pp. 3760–3763). Boston, MA, United States: IEEE. <a href=\"https://doi.org/10.1109/BigData.2017.8258375\">https://doi.org/10.1109/BigData.2017.8258375</a>","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: <i>2017 IEEE International Conference on Big Data</i>. IEEE; 2017:3760-3763. doi:<a href=\"https://doi.org/10.1109/BigData.2017.8258375\">10.1109/BigData.2017.8258375</a>","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” <i>2017 IEEE International Conference on Big Data</i>, IEEE, 2017, pp. 3760–63, doi:<a href=\"https://doi.org/10.1109/BigData.2017.8258375\">10.1109/BigData.2017.8258375</a>.","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In <i>2017 IEEE International Conference on Big Data</i>, 3760–63. IEEE, 2017. <a href=\"https://doi.org/10.1109/BigData.2017.8258375\">https://doi.org/10.1109/BigData.2017.8258375</a>.","ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in <i>2017 IEEE International Conference on Big Data</i>, Boston, MA, United States, 2017, pp. 3760–3763."},"department":[{"_id":"ChLa"}],"quality_controlled":"1","date_created":"2018-12-11T11:48:18Z","abstract":[{"lang":"eng","text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation."}],"language":[{"iso":"eng"}],"conference":{"end_date":"2017-12-14","start_date":"2017-12-11","name":"Big Data","location":"Boston, MA, United States"},"date_published":"2017-12-01T00:00:00Z","publication":"2017 IEEE International Conference on Big Data","date_updated":"2021-01-12T08:13:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"None","publication_identifier":{"isbn":["978-153862714-3"]},"status":"public","scopus_import":1,"year":"2017","title":"Optimal geospatial volunteer allocation needs realistic distances","page":"3760 - 3763","type":"conference","publist_id":"6906","doi":"10.1109/BigData.2017.8258375"},{"quality_controlled":"1","author":[{"last_name":"Matsubayashi","first_name":"Yutaka","full_name":"Matsubayashi, Yutaka"},{"last_name":"Louani","full_name":"Louani, Adam","first_name":"Adam"},{"first_name":"Anca","full_name":"Dragu, Anca","last_name":"Dragu"},{"last_name":"Sanchez Sanchez","first_name":"Besaiz","full_name":"Sanchez Sanchez, Besaiz"},{"last_name":"Serna Morales","full_name":"Serna Morales, Eduardo","first_name":"Eduardo"},{"last_name":"Yolland","full_name":"Yolland, Lawrence","first_name":"Lawrence"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","first_name":"Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vizcay","first_name":"Gema","full_name":"Vizcay, Gema"},{"last_name":"Fleck","full_name":"Fleck, Roland","first_name":"Roland"},{"last_name":"Heddleston","full_name":"Heddleston, John","first_name":"John"},{"last_name":"Chew","first_name":"Teng","full_name":"Chew, Teng"},{"first_name":"Daria E","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"},{"last_name":"Stramer","full_name":"Stramer, Brian","first_name":"Brian"}],"intvolume":"        27","month":"11","publication":"Current Biology","external_id":{"isi":["000415815800031"]},"date_published":"2017-11-09T00:00:00Z","oa_version":"Published Version","article_processing_charge":"No","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"},"publication_status":"published","file":[{"checksum":"264cf6c6c3551486ba5ea786850e000a","file_size":4770657,"date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","file_id":"4770","relation":"main_file","access_level":"open_access","file_name":"IST-2017-875-v1+1_1-s2.0-S0960982217312691-main.pdf","date_created":"2018-12-12T10:09:45Z","creator":"system"}],"has_accepted_license":"1","doi":"10.1016/j.cub.2017.10.001","year":"2017","ddc":["570","576"],"department":[{"_id":"DaSi"}],"citation":{"mla":"Matsubayashi, Yutaka, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” <i>Current Biology</i>, vol. 27, no. 22, Cell Press, 2017, p. 3526–3534e.4, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.10.001\">10.1016/j.cub.2017.10.001</a>.","chicago":"Matsubayashi, Yutaka, Adam Louani, Anca Dragu, Besaiz Sanchez Sanchez, Eduardo Serna Morales, Lawrence Yolland, Attila György, et al. “A Moving Source of Matrix Components Is Essential for De Novo Basement Membrane Formation.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.10.001\">https://doi.org/10.1016/j.cub.2017.10.001</a>.","ista":"Matsubayashi Y, Louani A, Dragu A, Sanchez Sanchez B, Serna Morales E, Yolland L, György A, Vizcay G, Fleck R, Heddleston J, Chew T, Siekhaus DE, Stramer B. 2017. A moving source of matrix components is essential for De Novo basement membrane formation. Current Biology. 27(22), 3526–3534e.4.","ieee":"Y. Matsubayashi <i>et al.</i>, “A moving source of matrix components is essential for De Novo basement membrane formation,” <i>Current Biology</i>, vol. 27, no. 22. Cell Press, p. 3526–3534e.4, 2017.","short":"Y. Matsubayashi, A. Louani, A. Dragu, B. Sanchez Sanchez, E. Serna Morales, L. Yolland, A. György, G. Vizcay, R. Fleck, J. Heddleston, T. Chew, D.E. Siekhaus, B. Stramer, Current Biology 27 (2017) 3526–3534e.4.","apa":"Matsubayashi, Y., Louani, A., Dragu, A., Sanchez Sanchez, B., Serna Morales, E., Yolland, L., … Stramer, B. (2017). A moving source of matrix components is essential for De Novo basement membrane formation. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.10.001\">https://doi.org/10.1016/j.cub.2017.10.001</a>","ama":"Matsubayashi Y, Louani A, Dragu A, et al. A moving source of matrix components is essential for De Novo basement membrane formation. <i>Current Biology</i>. 2017;27(22):3526-3534e.4. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.10.001\">10.1016/j.cub.2017.10.001</a>"},"day":"09","_id":"751","pubrep_id":"875","publisher":"Cell Press","date_updated":"2023-09-27T12:25:31Z","isi":1,"oa":1,"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:18Z","volume":27,"abstract":[{"text":"The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.","lang":"eng"}],"issue":"22","file_date_updated":"2020-07-14T12:47:59Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6905","type":"journal_article","scopus_import":"1","title":"A moving source of matrix components is essential for De Novo basement membrane formation","publication_identifier":{"issn":["09609822"]},"status":"public","page":"3526 - 3534e.4"},{"scopus_import":"1","status":"public","publication_identifier":{"isbn":["978-145034992-5"]},"title":"The power of choice in priority scheduling","page":"283 - 292","publist_id":"6864","type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between &quot;heavily loaded&quot; balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance."}],"date_created":"2018-12-11T11:48:31Z","volume":"Part F129314","language":[{"iso":"eng"}],"isi":1,"oa":1,"date_updated":"2023-09-27T12:17:59Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04178"}],"day":"26","_id":"791","publisher":"ACM","citation":{"short":"D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., &#38; Nadiradze, G. (2017). The power of choice in priority scheduling. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>","ama":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Vol Part F129314. ACM; 2017:283-292. doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>","mla":"Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, vol. Part F129314, ACM, 2017, pp. 283–92, doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Part F129314:283–92. ACM, 2017. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>.","ista":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292."},"department":[{"_id":"DaAl"}],"year":"2017","doi":"10.1145/3087801.3087810","publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","conference":{"start_date":"2017-07-25","end_date":"2017-07-27","name":"PODC: Principles of Distributed Computing","location":"Washington, WA, USA"},"date_published":"2017-07-26T00:00:00Z","publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","external_id":{"isi":["000462995000035"]},"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"first_name":"Giorgi","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"month":"07","quality_controlled":"1"},{"_id":"792","publisher":"Cambridge University Press","day":"25","citation":{"mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>.","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>.","ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301.","ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 833. Cambridge University Press, pp. 274–301, 2017.","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301.","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., &#38; Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;833:274-301. doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>"},"department":[{"_id":"BjHo"}],"volume":833,"abstract":[{"lang":"eng","text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at   Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics."}],"date_created":"2018-12-11T11:48:32Z","language":[{"iso":"eng"}],"oa":1,"isi":1,"date_updated":"2023-09-27T12:17:35Z","main_file_link":[{"url":"https://arxiv.org/abs/1705.03720","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"274 - 301","publication_identifier":{"issn":["00221120"]},"scopus_import":"1","title":"Relative periodic orbits form the backbone of turbulent pipe flow","status":"public","publist_id":"6862","type":"journal_article","author":[{"orcid":"0000-0003-0423-5010","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Short","first_name":"Kimberly","full_name":"Short, Kimberly"},{"last_name":"Farazmand","full_name":"Farazmand, Mohammad","first_name":"Mohammad"},{"last_name":"Willis","full_name":"Willis, Ashley","first_name":"Ashley"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"month":"12","intvolume":"       833","quality_controlled":"1","date_published":"2017-12-25T00:00:00Z","publication":"Journal of Fluid Mechanics","external_id":{"isi":["000414641700001"]},"publication_status":"published","article_processing_charge":"No","project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"oa_version":"Submitted Version","year":"2017","doi":"10.1017/jfm.2017.699"},{"month":"01","intvolume":"        66","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mojarrad","first_name":"Hossein","full_name":"Mojarrad, Hossein"},{"last_name":"Naszódi","full_name":"Naszódi, Márton","first_name":"Márton"},{"last_name":"Solymosi","full_name":"Solymosi, József","first_name":"József"},{"full_name":"Stich, Sebastian","first_name":"Sebastian","last_name":"Stich"},{"first_name":"May","full_name":"Szedlák, May","last_name":"Szedlák"}],"quality_controlled":"1","publication":"Computational Geometry: Theory and Applications","external_id":{"isi":["000412039700003"]},"date_published":"2017-01-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1016/j.comgeo.2017.07.002","year":"2017","citation":{"chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>.","ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 28–31, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 28–31, 2017.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., &#38; Szedlák, M. (2017). On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. 2017;66:28-31. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31."},"day":"01","publisher":"Elsevier","_id":"793","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"volume":66,"abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c &gt; 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}],"date_created":"2018-12-11T11:48:32Z","date_updated":"2023-09-27T12:15:16Z","main_file_link":[{"url":"https://arxiv.org/abs/1701.08183","open_access":"1"}],"isi":1,"oa":1,"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6861","type":"journal_article","title":"On the existence of ordinary triangles","status":"public","publication_identifier":{"issn":["09257721"]},"page":"28 - 31"},{"intvolume":"        66","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"}],"month":"12","quality_controlled":"1","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result.","external_id":{"isi":["000412039700001"]},"publication":"Computational Geometry: Theory and Applications","date_published":"2017-12-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"Preprint","related_material":{"record":[{"id":"1165","relation":"earlier_version","status":"public"}]},"doi":"10.1016/j.comgeo.2017.06.016","year":"2017","citation":{"ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 1–13, 2017.","mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 1–13, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>.","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. 2017;66:1-13. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>","short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13."},"day":"01","publisher":"Elsevier","_id":"794","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:32Z","volume":66,"abstract":[{"lang":"eng","text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle."}],"date_updated":"2023-09-27T12:14:49Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"isi":1,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","publist_id":"6860","scopus_import":"1","status":"public","title":"C-planarity of embedded cyclic c-graphs","page":"1 - 13"},{"publist_id":"6859","type":"journal_article","publication_identifier":{"issn":["10778926"]},"title":"Unified Hanani Tutte theorem","scopus_import":"1","status":"public","file_date_updated":"2020-07-14T12:48:06Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","language":[{"iso":"eng"}],"volume":24,"date_created":"2018-12-11T11:48:32Z","abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"date_updated":"2022-03-18T12:58:53Z","article_type":"original","oa":1,"citation":{"short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017).","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. 2017;24(3). doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>","apa":"Fulek, R., Kynčl, J., &#38; Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. International Press. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, 2017.","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3, P3.18, International Press, 2017, doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>.","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>. International Press, 2017. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>."},"publisher":"International Press","_id":"795","day":"28","department":[{"_id":"UlWa"}],"ddc":["000"],"doi":"10.37236/6663","has_accepted_license":"1","file":[{"access_level":"open_access","creator":"dernst","file_name":"2017_ElectrCombi_Fulek.pdf","date_created":"2019-01-18T14:04:08Z","content_type":"application/pdf","file_id":"5853","date_updated":"2020-07-14T12:48:06Z","relation":"main_file","checksum":"ef320cff0f062051e858f929be6a3581","file_size":236944}],"year":"2017","article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Electronic Journal of Combinatorics","date_published":"2017-07-28T00:00:00Z","intvolume":"        24","month":"07","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"quality_controlled":"1","article_number":"P3.18"},{"publist_id":"6857","type":"journal_article","title":"Al transmon qubits on silicon on insulator for quantum device integration","scopus_import":"1","status":"public","publication_identifier":{"issn":["00036951"]},"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-27T12:13:36Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.10195"}],"oa":1,"isi":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon."}],"volume":111,"date_created":"2018-12-11T11:48:33Z","department":[{"_id":"JoFi"}],"citation":{"apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., &#38; Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. 2017;111(4). doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017).","chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>.","mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>.","ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603.","ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” <i>Applied Physics Letters</i>, vol. 111, no. 4. American Institute of Physics, 2017."},"_id":"796","publisher":"American Institute of Physics","day":"01","doi":"10.1063/1.4994661","year":"2017","oa_version":"Submitted Version","article_processing_charge":"No","publication_status":"published","publication":"Applied Physics Letters","external_id":{"isi":["000406779700031"]},"date_published":"2017-07-01T00:00:00Z","acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","quality_controlled":"1","article_number":"042603","author":[{"full_name":"Keller, Andrew J","first_name":"Andrew J","last_name":"Keller"},{"full_name":"Dieterle, Paul","first_name":"Paul","last_name":"Dieterle"},{"last_name":"Fang","full_name":"Fang, Michael","first_name":"Michael"},{"last_name":"Berger","first_name":"Brett","full_name":"Berger, Brett"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"}],"month":"07","intvolume":"       111"},{"day":"01","publisher":"Wiley","_id":"797","month":"05","intvolume":"        48","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"citation":{"ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” <i>Physik in unserer Zeit</i>, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. <i>Physik in Unserer Zeit</i>. Wiley. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>","ama":"Fink JM. Photonenblockade aufgelöst. <i>Physik in unserer Zeit</i>. 2017;48(3):111-113. doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113."},"department":[{"_id":"JoFi"}],"quality_controlled":"1","volume":48,"date_created":"2018-12-11T11:48:33Z","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","publication":"Physik in unserer Zeit","date_updated":"2022-03-24T09:16:20Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","oa_version":"None","issue":"3","status":"public","year":"2017","title":"Photonenblockade aufgelöst","page":"111 - 113","publist_id":"6856","type":"journal_article","doi":"10.1002/piuz.201770305"},{"oa":1,"isi":1,"date_updated":"2023-09-27T12:11:28Z","volume":8,"abstract":[{"lang":"eng","text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout."}],"date_created":"2018-12-11T11:48:33Z","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"_id":"798","publisher":"Nature Publishing Group","pubrep_id":"867","day":"16","citation":{"ieee":"S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>.","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>.","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017)."},"status":"public","scopus_import":"1","publication_identifier":{"issn":["20411723"]},"title":"Mechanical on chip microwave circulator","type":"journal_article","publist_id":"6855","issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:48:06Z","ec_funded":1,"date_published":"2017-10-16T00:00:00Z","external_id":{"isi":["000412999700021"]},"publication":"Nature Communications","article_number":"1304","quality_controlled":"1","author":[{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"full_name":"Dieterle, Paul","first_name":"Paul","last_name":"Dieterle"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"intvolume":"         8","month":"10","year":"2017","doi":"10.1038/s41467-017-01304-x","file":[{"file_size":1467696,"checksum":"b68dafa71d1834c23b742cd9987a3d5f","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","date_created":"2018-12-12T10:15:25Z","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:06Z","content_type":"application/pdf","file_id":"5145"}],"has_accepted_license":"1","ddc":["539"],"project":[{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_status":"published","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"},"article_processing_charge":"Yes (in subscription journal)"},{"file_date_updated":"2020-07-14T12:48:06Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"10","type":"journal_article","publist_id":"6854","scopus_import":"1","publication_identifier":{"issn":["00320781"]},"title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","status":"public","citation":{"short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. 2017;58(10). doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>","ieee":"S. Kitakura <i>et al.</i>, “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” <i>Plant and Cell Physiology</i>, vol. 58, no. 10. Oxford University Press, 2017.","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>.","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811."},"_id":"799","publisher":"Oxford University Press","pubrep_id":"1009","day":"21","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"volume":58,"date_created":"2018-12-11T11:48:34Z","abstract":[{"lang":"eng","text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis."}],"date_updated":"2023-09-27T11:00:19Z","oa":1,"isi":1,"article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","ddc":["581"],"doi":"10.1093/pcp/pcx118","file":[{"file_id":"6333","date_updated":"2020-07-14T12:48:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2017_PlantCellPhysio_Kitakura.pdf","date_created":"2019-04-17T07:52:34Z","creator":"dernst","checksum":"bd3e3a94d55416739cbb19624bb977f8","file_size":1352913}],"has_accepted_license":"1","year":"2017","author":[{"last_name":"Kitakura","first_name":"Saeko","full_name":"Kitakura, Saeko"},{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","first_name":"Maciek","orcid":"0000-0001-6463-5257"},{"full_name":"Matsuura, Yuki","first_name":"Yuki","last_name":"Matsuura"},{"full_name":"Santuari, Luca","first_name":"Luca","last_name":"Santuari"},{"first_name":"Hirotaka","full_name":"Kouno, Hirotaka","last_name":"Kouno"},{"last_name":"Arima","full_name":"Arima, Kohei","first_name":"Kohei"},{"last_name":"Hardtke","first_name":"Christian","full_name":"Hardtke, Christian"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kakimoto","first_name":"Tatsuo","full_name":"Kakimoto, Tatsuo"},{"first_name":"Hirokazu","full_name":"Tanaka, Hirokazu","last_name":"Tanaka"}],"intvolume":"        58","month":"08","quality_controlled":"1","article_number":"1801-1811","pmid":1,"publication":"Plant and Cell Physiology","external_id":{"isi":["000413220400019"],"pmid":["29016942"]},"date_published":"2017-08-21T00:00:00Z"},{"ddc":["571"],"year":"2017","doi":"10.1038/s41467-017-00936-3","file":[{"checksum":"7e2c7621afd5f802338e92e8619f024d","file_size":4261832,"file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","date_created":"2018-12-12T10:15:17Z","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:48:07Z","content_type":"application/pdf","file_id":"5135"}],"has_accepted_license":"1","publication_status":"published","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"},"article_processing_charge":"No","project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","date_published":"2017-10-02T00:00:00Z","publication":"Nature Communications","external_id":{"isi":["000412053100004"]},"intvolume":"         8","month":"10","author":[{"full_name":"Strüber, Michael","first_name":"Michael","last_name":"Strüber"},{"last_name":"Sauer","full_name":"Sauer, Jonas","first_name":"Jonas"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bartos, Marlene","first_name":"Marlene","last_name":"Bartos"}],"article_number":"758","quality_controlled":"1","title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","publication_identifier":{"issn":["20411723"]},"scopus_import":"1","status":"public","publist_id":"6853","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"file_date_updated":"2020-07-14T12:48:07Z","issue":"1","abstract":[{"text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.","lang":"eng"}],"volume":8,"date_created":"2018-12-11T11:48:34Z","language":[{"iso":"eng"}],"oa":1,"isi":1,"date_updated":"2023-09-27T10:59:41Z","publisher":"Nature Publishing Group","_id":"800","pubrep_id":"914","day":"02","citation":{"ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>.","chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>.","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","apa":"Strüber, M., Sauer, J., Jonas, P. M., &#38; Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>"},"department":[{"_id":"PeJo"}]},{"has_accepted_license":"1","file":[{"date_created":"2019-01-18T13:45:40Z","file_name":"2017_Cell_Samwer.pdf","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5852","date_updated":"2020-07-14T12:48:08Z","file_size":17666637,"checksum":"64897b0c5373f22273f598e4672c60ff"}],"doi":"10.1016/j.cell.2017.07.038","year":"2017","ddc":["570"],"oa_version":"Published Version","article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication_status":"published","external_id":{"isi":["000408372400014"]},"publication":"Cell","date_published":"2017-08-24T00:00:00Z","quality_controlled":"1","author":[{"last_name":"Samwer","full_name":"Samwer, Matthias","first_name":"Matthias"},{"last_name":"Schneider","first_name":"Maximilian","full_name":"Schneider, Maximilian"},{"first_name":"Rudolf","full_name":"Hoefler, Rudolf","last_name":"Hoefler"},{"orcid":"0000-0002-5795-0133","first_name":"Philipp S","full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst"},{"full_name":"Jude, Julian","first_name":"Julian","last_name":"Jude"},{"last_name":"Zuber","first_name":"Johannes","full_name":"Zuber, Johannes"},{"last_name":"Gerlic","first_name":"Daniel","full_name":"Gerlic, Daniel"}],"month":"08","intvolume":"       170","publist_id":"6848","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"}],"title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","publication_identifier":{"issn":["00928674"]},"status":"public","scopus_import":"1","page":"956 - 972","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"5","file_date_updated":"2020-07-14T12:48:08Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-27T10:59:14Z","isi":1,"oa":1,"language":[{"iso":"eng"}],"volume":170,"abstract":[{"text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function.","lang":"eng"}],"date_created":"2018-12-11T11:48:35Z","department":[{"_id":"CaHe"}],"citation":{"short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., &#38; Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. 2017;170(5):956-972. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972.","mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>.","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>.","ieee":"M. Samwer <i>et al.</i>, “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” <i>Cell</i>, vol. 170, no. 5. Cell Press, pp. 956–972, 2017."},"day":"24","_id":"803","publisher":"Cell Press"},{"type":"journal_article","publist_id":"6847","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","publication_identifier":{"issn":["15499618"]},"status":"public","page":"5039 - 5053","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"10","language":[{"iso":"eng"}],"volume":13,"date_created":"2018-12-11T11:48:35Z","abstract":[{"text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides.","lang":"eng"}],"date_updated":"2023-09-27T10:58:45Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.03773"}],"isi":1,"oa":1,"citation":{"ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>.","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>.","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38; Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>"},"day":"10","publisher":"American Chemical Society","_id":"804","department":[{"_id":"CaHe"}],"doi":"10.1021/acs.jctc.7b00374","year":"2017","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","external_id":{"isi":["000412965700036"]},"publication":"Journal of Chemical Theory and Computation","date_published":"2017-10-10T00:00:00Z","month":"10","author":[{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","first_name":"Philipp S"},{"last_name":"Deluweit","first_name":"Felix","full_name":"Deluweit, Felix"},{"first_name":"Roger","full_name":"Scherrers, Roger","last_name":"Scherrers"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        13","quality_controlled":"1"},{"date_published":"2017-10-31T00:00:00Z","isi":1,"date_updated":"2023-09-26T16:20:09Z","external_id":{"isi":["000414025600007"]},"publication":"Development","date_created":"2018-12-11T11:48:36Z","abstract":[{"text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2).","lang":"eng"}],"volume":144,"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"quality_controlled":"1","_id":"805","publisher":"Company of Biologists","day":"31","citation":{"ieee":"S. Pfurr <i>et al.</i>, “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” <i>Development</i>, vol. 144. Company of Biologists, pp. 3917–3931, 2017.","mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>.","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931.","chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. 2017;144:3917-3931. doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>","apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>","short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931."},"author":[{"last_name":"Pfurr","first_name":"Sabrina","full_name":"Pfurr, Sabrina"},{"last_name":"Chu","first_name":"Yu","full_name":"Chu, Yu"},{"first_name":"Christian","full_name":"Bohrer, Christian","last_name":"Bohrer"},{"last_name":"Greulich","first_name":"Franziska","full_name":"Greulich, Franziska"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","full_name":"Beattie, Robert J","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"first_name":"Könül","full_name":"Mammadzada, Könül","last_name":"Mammadzada"},{"last_name":"Hils","full_name":"Hils, Miriam","first_name":"Miriam"},{"full_name":"Arnold, Sebastian","first_name":"Sebastian","last_name":"Arnold"},{"last_name":"Taylor","full_name":"Taylor, Verdon","first_name":"Verdon"},{"last_name":"Schachtrup","full_name":"Schachtrup, Kristina","first_name":"Kristina"},{"first_name":"N Henriette","full_name":"Uhlenhaut, N Henriette","last_name":"Uhlenhaut"},{"last_name":"Schachtrup","first_name":"Christian","full_name":"Schachtrup, Christian"}],"month":"10","intvolume":"       144","page":"3917 - 3931","scopus_import":"1","year":"2017","status":"public","title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","doi":"10.1242/dev.145698","type":"journal_article","publist_id":"6846","oa_version":"None","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No"},{"publist_id":"6843","type":"journal_article","page":"274 - 280","publication_identifier":{"issn":["10222588"]},"scopus_import":1,"status":"public","title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","file_date_updated":"2020-07-14T12:48:09Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"2","language":[{"iso":"eng"}],"abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group &quot;Springer Compact Evaluierung&quot; made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"date_created":"2018-12-11T11:48:36Z","volume":70,"date_updated":"2021-01-12T08:16:45Z","oa":1,"citation":{"chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","apa":"Andrae, M., &#38; Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2017;70(2):274-280. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280."},"publisher":"VÖB","_id":"807","day":"01","department":[{"_id":"E-Lib"}],"popular_science":"1","ddc":["020"],"doi":"10.31263/voebm.v70i2.1898","has_accepted_license":"1","file":[{"checksum":"558c18bcf5580d87dd371ec626d52075","file_size":125065,"relation":"main_file","date_updated":"2020-07-14T12:48:09Z","file_id":"5851","content_type":"application/pdf","creator":"dernst","date_created":"2019-01-18T13:39:26Z","file_name":"2017_VOEB_Andrae.pdf","access_level":"open_access"}],"year":"2017","publication_status":"published","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_version":"Published Version","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","date_published":"2017-08-01T00:00:00Z","author":[{"last_name":"Andrae","first_name":"Magdalena","full_name":"Andrae, Magdalena"},{"first_name":"Márton","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","last_name":"Villányi"}],"intvolume":"        70","month":"08"},{"degree_awarded":"PhD","date_published":"2017-09-27T00:00:00Z","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","first_name":"Karin","full_name":"Mitosch, Karin"}],"month":"09","has_accepted_license":"1","file":[{"creator":"dernst","file_name":"Thesis_KarinMitosch.docx","date_created":"2019-04-05T08:48:51Z","access_level":"closed","relation":"source_file","date_updated":"2020-07-14T12:48:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6210","file_size":6331071,"checksum":"da3993c5f90f59a8e8623cc31ad501dd"},{"file_size":9289852,"checksum":"24c3d9e51992f1b721f3df55aa13fcb8","creator":"dernst","date_created":"2019-04-05T08:48:51Z","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","relation":"main_file","file_id":"6211","content_type":"application/pdf","date_updated":"2020-07-14T12:48:09Z"}],"doi":"10.15479/AT:ISTA:th_862","supervisor":[{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"year":"2017","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2001"},{"status":"public","relation":"part_of_dissertation","id":"666"}]},"ddc":["571","579"],"oa_version":"Published Version","article_processing_charge":"No","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"},"publication_status":"published","date_updated":"2023-09-07T12:00:26Z","oa":1,"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:40Z","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"ToBo"}],"citation":{"short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017."},"day":"27","_id":"818","pubrep_id":"862","publisher":"Institute of Science and Technology Austria","publist_id":"6831","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","status":"public","page":"113","file_date_updated":"2020-07-14T12:48:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]