[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Ivanov, G., & Tsiutsiurupa, I. (2021). Functional Löwner ellipsoids. Journal of Geometric Analysis. Springer. https://doi.org/10.1007/s12220-021-00691-4","ama":"Ivanov G, Tsiutsiurupa I. Functional Löwner ellipsoids. Journal of Geometric Analysis. 2021;31:11493-11528. doi:10.1007/s12220-021-00691-4","ieee":"G. Ivanov and I. Tsiutsiurupa, “Functional Löwner ellipsoids,” Journal of Geometric Analysis, vol. 31. Springer, pp. 11493–11528, 2021.","short":"G. Ivanov, I. Tsiutsiurupa, Journal of Geometric Analysis 31 (2021) 11493–11528.","mla":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis, vol. 31, Springer, 2021, pp. 11493–528, doi:10.1007/s12220-021-00691-4.","ista":"Ivanov G, Tsiutsiurupa I. 2021. Functional Löwner ellipsoids. Journal of Geometric Analysis. 31, 11493–11528.","chicago":"Ivanov, Grigory, and Igor Tsiutsiurupa. “Functional Löwner Ellipsoids.” Journal of Geometric Analysis. Springer, 2021. https://doi.org/10.1007/s12220-021-00691-4."},"title":"Functional Löwner ellipsoids","article_processing_charge":"No","external_id":{"arxiv":["2008.09543"],"isi":["000656507500001"]},"author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory","last_name":"Ivanov"},{"first_name":"Igor","full_name":"Tsiutsiurupa, Igor","last_name":"Tsiutsiurupa"}],"acknowledgement":"The authors acknowledge the support of the grant of the Russian Government N 075-15-2019-1926.","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Journal of Geometric Analysis","day":"31","year":"2021","isi":1,"date_created":"2021-06-13T22:01:32Z","doi":"10.1007/s12220-021-00691-4","date_published":"2021-05-31T00:00:00Z","page":"11493-11528","_id":"9548","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-08T14:04:49Z","department":[{"_id":"UlWa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it."}],"intvolume":" 31","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.09543"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1559-002X"],"issn":["1050-6926"]},"volume":31},{"status":"public","type":"research_data_reference","_id":"13080","title":"Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire","department":[{"_id":"AnHi"}],"article_processing_charge":"No","author":[{"last_name":"Puglia","full_name":"Puglia, Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise"},{"first_name":"Esteban","last_name":"Martinez","full_name":"Martinez, Esteban"},{"last_name":"Menard","full_name":"Menard, Gerbold","first_name":"Gerbold"},{"first_name":"Andreas","full_name":"Pöschl, Andreas","last_name":"Pöschl"},{"first_name":"Sergei","full_name":"Gronin, Sergei","last_name":"Gronin"},{"first_name":"Geoffrey","last_name":"Gardner","full_name":"Gardner, Geoffrey"},{"first_name":"Ray","last_name":"Kallaher","full_name":"Kallaher, Ray"},{"full_name":"Manfra, Michael","last_name":"Manfra","first_name":"Michael"},{"last_name":"Marcus","full_name":"Marcus, Charles","first_name":"Charles"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"},{"first_name":"Lucas","last_name":"Casparis","full_name":"Casparis, Lucas"}],"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.","ista":"Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.","mla":"Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.","short":"D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).","ieee":"D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021.","ama":"Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435","apa":"Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435"},"date_updated":"2023-08-08T14:08:07Z","month":"03","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4592460","open_access":"1"}],"publisher":"Zenodo","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well."}],"date_created":"2023-05-23T17:11:28Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9570"}],"link":[{"url":"https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3","relation":"software"}]},"doi":"10.5281/ZENODO.4592435","date_published":"2021-03-09T00:00:00Z","day":"09","year":"2021"},{"date_updated":"2023-08-08T14:23:21Z","ddc":["540"],"department":[{"_id":"KiMo"}],"file_date_updated":"2021-06-23T13:09:34Z","_id":"9569","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2046-2069"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9596","checksum":"cd582d67ace7151078e46b3a896871a9","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-06-23T13:09:34Z","file_name":"2021_RSCAdvances_Dar.pdf","creator":"asandaue","date_updated":"2021-06-23T13:09:34Z","file_size":2114557}],"license":"https://creativecommons.org/licenses/by/3.0/","issue":"35","volume":11,"abstract":[{"text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values.","lang":"eng"}],"oa_version":"Published Version","intvolume":" 11","month":"06","citation":{"mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:10.1039/d1ra03428f.","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","ieee":"M. S. Dar et al., “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” RSC Advances, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021.","ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 2021;11(35):21702-21715. doi:10.1039/d1ra03428f","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/d1ra03428f","chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” RSC Advances. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1ra03428f.","ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000665644000048"]},"author":[{"first_name":"M. S.","last_name":"Dar","full_name":"Dar, M. S."},{"full_name":"Akram, Khush Bakhat","last_name":"Akram","first_name":"Khush Bakhat"},{"last_name":"Sohail","full_name":"Sohail, Ayesha","first_name":"Ayesha"},{"first_name":"Fatima","last_name":"Arif","full_name":"Arif, Fatima"},{"full_name":"Zabihi, Fatemeh","last_name":"Zabihi","first_name":"Fatemeh"},{"full_name":"Yang, Shengyuan","last_name":"Yang","first_name":"Shengyuan"},{"first_name":"Shamsa","last_name":"Munir","full_name":"Munir, Shamsa"},{"last_name":"Zhu","full_name":"Zhu, Meifang","first_name":"Meifang"},{"full_name":"Abid, M.","last_name":"Abid","first_name":"M."},{"first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","last_name":"Nauman"}],"title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","year":"2021","has_accepted_license":"1","isi":1,"publication":"RSC Advances","day":"18","page":"21702-21715","date_created":"2021-06-19T07:27:45Z","doi":"10.1039/d1ra03428f","date_published":"2021-06-18T00:00:00Z","acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1"},{"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"18","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.126.244502","date_published":"2021-06-18T00:00:00Z","date_created":"2021-06-16T15:45:36Z","article_number":"244502","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"citation":{"ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/PhysRevLett.126.244502.","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” Physical Review Letters, vol. 126, no. 24. American Physical Society, 2021.","short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","apa":"Yalniz, G., Hof, B., & Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.126.244502","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 2021;126(24). doi:10.1103/PhysRevLett.126.244502","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” Physical Review Letters, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:10.1103/PhysRevLett.126.244502."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Yalniz","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"}],"external_id":{"isi":["000663310100008"],"arxiv":["2007.02584"]},"article_processing_charge":"No","title":"Coarse graining the state space of a turbulent flow using periodic orbits","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"month":"06","intvolume":" 126","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"24","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/"}]},"volume":126,"_id":"9558","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-08-08T14:08:36Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}]},{"author":[{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"full_name":"Gilis, Anja","last_name":"Gilis","first_name":"Anja"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"first_name":"Javier","full_name":"Guillén, Javier","last_name":"Guillén"},{"last_name":"Castagné","full_name":"Castagné, Vincent","first_name":"Vincent"},{"last_name":"Lefevre","full_name":"Lefevre, Isabel A.","first_name":"Isabel A."},{"first_name":"Fiona","last_name":"Ducrey","full_name":"Ducrey, Fiona"},{"last_name":"Monk","full_name":"Monk, Lee","first_name":"Lee"},{"first_name":"Sandrine","full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni"},{"first_name":"Bruce","last_name":"Altevogt","full_name":"Altevogt, Bruce"},{"first_name":"María","last_name":"Arroyo-Araujo","full_name":"Arroyo-Araujo, María"},{"last_name":"Bikovski","full_name":"Bikovski, Lior","first_name":"Lior"},{"last_name":"De Bruin","full_name":"De Bruin, Natasja","first_name":"Natasja"},{"last_name":"Castaños-Vélez","full_name":"Castaños-Vélez, Esmeralda","first_name":"Esmeralda"},{"full_name":"Dityatev, Alexander","last_name":"Dityatev","first_name":"Alexander"},{"full_name":"Emmerich, Christoph H.","last_name":"Emmerich","first_name":"Christoph H."},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"first_name":"Chantelle","full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham"},{"first_name":"Christelle","full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux"},{"first_name":"Valerie","last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie"},{"full_name":"Hölter, Sabine M.","last_name":"Hölter","first_name":"Sabine M."},{"last_name":"Hofmann","full_name":"Hofmann, Martine Cj","first_name":"Martine Cj"},{"last_name":"Kabitzke","full_name":"Kabitzke, Patricia","first_name":"Patricia"},{"first_name":"Martien Jh","full_name":"Kas, Martien Jh","last_name":"Kas"},{"last_name":"Kurreck","full_name":"Kurreck, Claudia","first_name":"Claudia"},{"first_name":"Paul","last_name":"Moser","full_name":"Moser, Paul"},{"full_name":"Pietraszek, Malgorzata","last_name":"Pietraszek","first_name":"Malgorzata"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"first_name":"Heidrun","full_name":"Potschka, Heidrun","last_name":"Potschka"},{"first_name":"Ernesto","full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca"},{"last_name":"Restivo","full_name":"Restivo, Leonardo","first_name":"Leonardo"},{"full_name":"Riedel, Gernot","last_name":"Riedel","first_name":"Gernot"},{"full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga","first_name":"Merel"},{"first_name":"Janko","full_name":"Samardzic, Janko","last_name":"Samardzic"},{"id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Schunn","full_name":"Schunn, Michael","orcid":"0000-0003-4326-5300"},{"full_name":"Stöger, Claudia","last_name":"Stöger","first_name":"Claudia"},{"first_name":"Vootele","full_name":"Voikar, Vootele","last_name":"Voikar"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"last_name":"Wever","full_name":"Wever, Kimberley E.","first_name":"Kimberley E."},{"first_name":"Kathleen","last_name":"Wuyts","full_name":"Wuyts, Kathleen"},{"first_name":"Malcolm R.","last_name":"Macleod","full_name":"Macleod, Malcolm R."},{"first_name":"Ulrich","full_name":"Dirnagl, Ulrich","last_name":"Dirnagl"},{"first_name":"Thomas","last_name":"Steckler","full_name":"Steckler, Thomas"}],"article_processing_charge":"No","external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"title":"Introduction to the EQIPD quality system","citation":{"apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.7554/eLife.63294","date_published":"2021-05-24T00:00:00Z","date_created":"2021-06-27T22:01:49Z","has_accepted_license":"1","isi":1,"year":"2021","day":"24","publication":"eLife","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","department":[{"_id":"PreCl"}],"file_date_updated":"2021-06-28T11:35:30Z","date_updated":"2023-08-10T13:36:50Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9607","volume":10,"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file":[{"date_created":"2021-06-28T11:35:30Z","file_name":"2021_ELife_Bespalov.pdf","date_updated":"2021-06-28T11:35:30Z","file_size":2500720,"creator":"asandaue","checksum":"885b746051a7a6b6e24e3d2781a48fde","file_id":"9609","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 10","abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"oa_version":"Published Version","pmid":1},{"publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"75dd89d09945185b2d14b2434a0bcb50","file_id":"9608","success":1,"date_updated":"2021-06-28T08:04:22Z","file_size":2156554,"creator":"asandaue","date_created":"2021-06-28T08:04:22Z","file_name":"2021_NatureCommunications_Santini.pdf"}],"issue":"1","volume":12,"abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"07","date_updated":"2023-08-10T13:53:23Z","ddc":["570"],"file_date_updated":"2021-06-28T08:04:22Z","department":[{"_id":"SiHi"}],"_id":"9601","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","year":"2021","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"12","date_created":"2021-06-27T22:01:46Z","date_published":"2021-07-12T00:00:00Z","doi":"10.1038/s41467-021-23510-4","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23510-4.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23510-4","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23510-4","ieee":"L. Santini et al., “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” Nature Communications, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:10.1038/s41467-021-23510-4."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000667248600005"]},"author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"last_name":"Asami","full_name":"Asami, Maki","first_name":"Maki"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"last_name":"Ramesmayer","full_name":"Ramesmayer, Julia","first_name":"Julia"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"first_name":"Nick","full_name":"Warr, Nick","last_name":"Warr"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Laue","full_name":"Laue, Ernest","first_name":"Ernest"},{"first_name":"Matthias","full_name":"Farlik, Matthias","last_name":"Farlik"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"first_name":"Andreas","full_name":"Beyer, Andreas","last_name":"Beyer"},{"last_name":"Perry","full_name":"Perry, Anthony C.F.","first_name":"Anthony C.F."},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"}],"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","article_number":"3804"},{"_id":"9602","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-08-10T13:38:00Z","file_date_updated":"2021-06-28T13:33:23Z","department":[{"_id":"HeEd"}],"oa_version":"Published Version","abstract":[{"text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees.","lang":"eng"}],"intvolume":" 151","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"asandaue","file_size":418168,"date_updated":"2021-06-28T13:33:23Z","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","date_created":"2021-06-28T13:33:23Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","file_id":"9612"}],"publication_status":"published","publication_identifier":{"issn":["0095-8956"]},"volume":151,"project":[{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory Series B. 2021;151:21-37. doi:10.1016/j.jctb.2021.05.004","apa":"Pach, J., & Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. Elsevier. https://doi.org/10.1016/j.jctb.2021.05.004","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” Journal of Combinatorial Theory. Series B, vol. 151. Elsevier, pp. 21–37, 2021.","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B, vol. 151, Elsevier, 2021, pp. 21–37, doi:10.1016/j.jctb.2021.05.004.","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” Journal of Combinatorial Theory. Series B. Elsevier, 2021. https://doi.org/10.1016/j.jctb.2021.05.004."},"title":"Erdős-Hajnal-type results for monotone paths","article_processing_charge":"No","external_id":{"isi":["000702280800002"]},"author":[{"full_name":"Pach, János","last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"},{"last_name":"Tomon","full_name":"Tomon, István","first_name":"István"}],"acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Journal of Combinatorial Theory. Series B","day":"09","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-06-27T22:01:47Z","date_published":"2021-06-09T00:00:00Z","doi":"10.1016/j.jctb.2021.05.004","page":"21-37"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"issue":"6","volume":103,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results."}],"intvolume":" 103","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/2009.06491","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-10T13:37:25Z","department":[{"_id":"MiLe"}],"_id":"9606","status":"public","article_type":"letter_note","type":"journal_article","publication":"Physical Review A","day":"01","year":"2021","isi":1,"date_created":"2021-06-27T22:01:49Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1103/PhysRevA.103.L061303","acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A. American Physical Society, 2021. https://doi.org/10.1103/PhysRevA.103.L061303.","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 2021;103(6). doi:10.1103/PhysRevA.103.L061303","apa":"Tononi, A., Cappellaro, A., Bighin, G., & Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.103.L061303","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” Physical Review A, vol. 103, no. 6. American Physical Society, 2021.","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” Physical Review A, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:10.1103/PhysRevA.103.L061303."},"title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","article_processing_charge":"No","external_id":{"arxiv":["2009.06491"],"isi":["000662296700014"]},"author":[{"first_name":"A.","full_name":"Tononi, A.","last_name":"Tononi"},{"last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto"},{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L.","full_name":"Salasnich, L.","last_name":"Salasnich"}],"article_number":"L061303"},{"scopus_import":"1","intvolume":" 36","month":"07","abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"issue":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","description":"News on IST Homepage"}]},"volume":36,"publication_status":"published","publication_identifier":{"eissn":["22111247"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_CellReports_Venturino.pdf","date_created":"2021-07-19T13:32:17Z","creator":"cziletti","file_size":56388540,"date_updated":"2021-07-19T13:32:17Z","success":1,"file_id":"9693","checksum":"f056255f6d01fd9a86b5387635928173","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9642","department":[{"_id":"SaSi"}],"file_date_updated":"2021-07-19T13:32:17Z","date_updated":"2023-08-10T14:09:39Z","ddc":["570"],"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","date_created":"2021-07-11T22:01:16Z","date_published":"2021-07-06T00:00:00Z","doi":"10.1016/j.celrep.2021.109313","year":"2021","has_accepted_license":"1","isi":1,"publication":"Cell Reports","day":"06","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"109313","article_processing_charge":"No","external_id":{"isi":["000670188500004"],"pmid":["34233180"]},"author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino"},{"first_name":"Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X"},{"last_name":"De Jesús-Cortés","full_name":"De Jesús-Cortés, Héctor","first_name":"Héctor"},{"full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","full_name":"Nagy, Balint","last_name":"Nagy"},{"last_name":"Reilly-Andújar","full_name":"Reilly-Andújar, Francis","first_name":"Francis"},{"full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","last_name":"Colombo","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E"},{"full_name":"Bear, Mark F.","last_name":"Bear","first_name":"Mark F."},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","citation":{"ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports. Elsevier, 2021. https://doi.org/10.1016/j.celrep.2021.109313.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","ieee":"A. Venturino et al., “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” Cell Reports, vol. 36, no. 1. Elsevier, 2021.","ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 2021;36(1). doi:10.1016/j.celrep.2021.109313","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2021.109313","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” Cell Reports, vol. 36, no. 1, 109313, Elsevier, 2021, doi:10.1016/j.celrep.2021.109313."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_id":"9613","file_size":7653149,"date_updated":"2021-06-28T14:06:24Z","creator":"asandaue","file_name":"2021_CellReports_Contreras.pdf","date_created":"2021-06-28T14:06:24Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22111247"]},"publication_status":"published","volume":35,"issue":"12","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"month":"06","intvolume":" 35","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-10T13:55:00Z","file_date_updated":"2021-06-28T14:06:24Z","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"_id":"9603","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"22","publication":"Cell Reports","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1016/j.celrep.2021.109274","date_published":"2021-06-22T00:00:00Z","date_created":"2021-06-27T22:01:48Z","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","quality_controlled":"1","publisher":"Cell Press","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274"},"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Davaatseren, Amarbayasgalan","last_name":"Davaatseren","first_name":"Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H"},{"id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","first_name":"Johanna","last_name":"Sonntag","full_name":"Sonntag, Johanna"},{"full_name":"Andersen, Lill","last_name":"Andersen","first_name":"Lill"},{"last_name":"Bernthaler","full_name":"Bernthaler, Tina","first_name":"Tina"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"last_name":"Heger","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena"},{"full_name":"Johnson, Randy L.","last_name":"Johnson","first_name":"Randy L."},{"last_name":"Schwarz","full_name":"Schwarz, Lindsay A.","first_name":"Lindsay A."},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"external_id":{"isi":["000664463600016"]},"article_processing_charge":"No","article_number":"109274","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}]},{"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"citation":{"mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:10.1126/science.abg2530.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. AAAS. https://doi.org/10.1126/science.abg2530","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 2021;371(6536):1355-1359. doi:10.1126/science.abg2530","ieee":"D. Bluvstein et al., “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” Science, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” Science. AAAS, 2021. https://doi.org/10.1126/science.abg2530.","ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2012.12276"],"isi":["000636043400048"],"pmid":["33632894"]},"article_processing_charge":"No","author":[{"first_name":"D.","last_name":"Bluvstein","full_name":"Bluvstein, D."},{"first_name":"A.","last_name":"Omran","full_name":"Omran, A."},{"last_name":"Levine","full_name":"Levine, H.","first_name":"H."},{"full_name":"Keesling, A.","last_name":"Keesling","first_name":"A."},{"first_name":"G.","last_name":"Semeghini","full_name":"Semeghini, G."},{"first_name":"S.","full_name":"Ebadi, S.","last_name":"Ebadi"},{"full_name":"Wang, T. T.","last_name":"Wang","first_name":"T. T."},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios"},{"last_name":"Maskara","full_name":"Maskara, N.","first_name":"N."},{"last_name":"Ho","full_name":"Ho, W. W.","first_name":"W. W."},{"first_name":"S.","last_name":"Choi","full_name":"Choi, S."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"M.","full_name":"Greiner, M.","last_name":"Greiner"},{"first_name":"V.","last_name":"Vuletić","full_name":"Vuletić, V."},{"first_name":"M. D.","last_name":"Lukin","full_name":"Lukin, M. D."}],"title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","oa":1,"quality_controlled":"1","publisher":"AAAS","year":"2021","has_accepted_license":"1","isi":1,"publication":"Science","day":"26","page":"1355-1359","date_created":"2021-06-29T12:04:05Z","date_published":"2021-03-26T00:00:00Z","doi":"10.1126/science.abg2530","_id":"9618","type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","date_updated":"2023-08-10T13:57:07Z","ddc":["539"],"file_date_updated":"2021-09-23T14:00:05Z","department":[{"_id":"MaSe"}],"abstract":[{"text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","intvolume":" 371","month":"03","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-23T14:00:05Z","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf","creator":"patrickd","date_updated":"2021-09-23T14:00:05Z","file_size":3671159,"checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","file_id":"10040","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":371,"issue":"6536"},{"has_accepted_license":"1","isi":1,"year":"2021","day":"07","publication":"Plant Cell","page":"2981–3003","doi":"10.1093/plcell/koab183","date_published":"2021-07-07T00:00:00Z","date_created":"2021-07-14T15:32:43Z","quality_controlled":"1","publisher":"American Society of Plant Biologists","oa":1,"citation":{"short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Gao","full_name":"Gao, Z","first_name":"Z"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"last_name":"Xu","full_name":"Xu, H","first_name":"H"},{"first_name":"Q","last_name":"Xu","full_name":"Xu, Q"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"full_name":"Huang, L","last_name":"Huang","first_name":"L"},{"first_name":"H","last_name":"Zhao","full_name":"Zhao, H"},{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"first_name":"S","full_name":"Mai, S","last_name":"Mai"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"first_name":"X","full_name":"Liu, X","last_name":"Liu"},{"first_name":"S","full_name":"Li, S","last_name":"Li"},{"first_name":"Y","full_name":"Guan, Y","last_name":"Guan"},{"full_name":"Yang, W","last_name":"Yang","first_name":"W"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"J","full_name":"Petrášek, J","last_name":"Petrášek"},{"first_name":"J","full_name":"Zhang, J","last_name":"Zhang"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"article_processing_charge":"No","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"publication_status":"published","file":[{"success":1,"file_id":"9691","checksum":"6715712ec306c321f0204c817b7f8ae7","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_PlantCell_Gao.pdf","date_created":"2021-07-19T12:13:34Z","creator":"cziletti","file_size":10566921,"date_updated":"2021-07-19T12:13:34Z"}],"language":[{"iso":"eng"}],"volume":33,"issue":"9","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"oa_version":"Published Version","pmid":1,"month":"07","intvolume":" 33","date_updated":"2023-08-10T14:01:41Z","ddc":["580"],"file_date_updated":"2021-07-19T12:13:34Z","department":[{"_id":"JiFr"}],"_id":"9657","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public"},{"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"4009","author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"article_processing_charge":"No","title":"Fast and strong amplifiers of natural selection","citation":{"mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:10.1038/s41467-021-24271-w.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-24271-w","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-24271-w","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-24271-w.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","date_published":"2021-06-29T00:00:00Z","doi":"10.1038/s41467-021-24271-w","date_created":"2021-07-11T22:01:15Z","has_accepted_license":"1","isi":1,"year":"2021","day":"29","publication":"Nature Communications","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9640","file_date_updated":"2021-07-19T13:02:20Z","department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:05:09Z","ddc":["510"],"scopus_import":"1","month":"06","intvolume":" 12","abstract":[{"lang":"eng","text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed."}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":12,"ec_funded":1,"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","file":[{"creator":"cziletti","file_size":628992,"date_updated":"2021-07-19T13:02:20Z","file_name":"2021_NatCoom_Tkadlec.pdf","date_created":"2021-07-19T13:02:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"5767418926a7f7fb76151de29473dae0","file_id":"9692"}],"language":[{"iso":"eng"}]},{"status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9656","file_date_updated":"2021-10-07T13:42:47Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2023-08-10T14:02:41Z","month":"10","intvolume":" 232","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"volume":232,"issue":"2","ec_funded":1,"file":[{"date_created":"2021-10-07T13:42:47Z","file_name":"2021_NewPhytologist_Han.pdf","date_updated":"2021-10-07T13:42:47Z","file_size":1939800,"creator":"kschuh","checksum":"6422a6eb329b52d96279daaee0fcf189","file_id":"10105","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"publication_status":"published","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","author":[{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617."},"publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","doi":"10.1111/nph.17617","date_published":"2021-10-01T00:00:00Z","date_created":"2021-07-14T15:29:14Z","page":"510-522","day":"01","publication":"New Phytologist","isi":1,"has_accepted_license":"1","year":"2021"},{"title":"Morphology of three-body quantum states from machine learning","external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"article_processing_charge":"Yes","author":[{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"first_name":"Oleksandr V.","full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov"},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” New Journal of Physics, vol. 23, no. 6. IOP Publishing, 2021.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. New Journal of Physics. 2021;23(6). doi:10.1088/1367-2630/ac0576","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., & Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac0576","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:10.1088/1367-2630/ac0576.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac0576."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"065009","date_created":"2021-07-18T22:01:22Z","date_published":"2021-06-23T00:00:00Z","doi":"10.1088/1367-2630/ac0576","publication":"New Journal of Physics","day":"23","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"publisher":"IOP Publishing","quality_controlled":"1","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","file_date_updated":"2021-07-19T11:47:16Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-08-10T13:58:09Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9679","ec_funded":1,"volume":23,"issue":"6","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9690","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","success":1,"date_updated":"2021-07-19T11:47:16Z","file_size":3868445,"creator":"cziletti","date_created":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["13672630"]},"intvolume":" 23","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}]},{"department":[{"_id":"EdHa"}],"date_updated":"2023-08-10T13:57:36Z","status":"public","article_type":"original","type":"journal_article","_id":"9629","ec_funded":1,"volume":23,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"intvolume":" 23","month":"06","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis."}],"title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","article_processing_charge":"No","external_id":{"pmid":["34155381"],"isi":["000664016300003"]},"author":[{"first_name":"Qiutan","last_name":"Yang","full_name":"Yang, Qiutan"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","full_name":"Xue, Shi-lei","last_name":"Xue"},{"full_name":"Chan, Chii Jou","last_name":"Chan","first_name":"Chii Jou"},{"last_name":"Rempfler","full_name":"Rempfler, Markus","first_name":"Markus"},{"last_name":"Vischi","full_name":"Vischi, Dario","first_name":"Dario"},{"full_name":"Maurer-Gutierrez, Francisca","last_name":"Maurer-Gutierrez","first_name":"Francisca"},{"full_name":"Hiiragi, Takashi","last_name":"Hiiragi","first_name":"Takashi"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Prisca","full_name":"Liberali, Prisca","last_name":"Liberali"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology. Springer Nature, 2021. https://doi.org/10.1038/s41556-021-00700-2.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” Nature Cell Biology, vol. 23, Springer Nature, 2021, pp. 733–744, doi:10.1038/s41556-021-00700-2.","ieee":"Q. Yang et al., “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” Nature Cell Biology, vol. 23. Springer Nature, pp. 733–744, 2021.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-021-00700-2","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 2021;23:733–744. doi:10.1038/s41556-021-00700-2"},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-07-04T22:01:25Z","date_published":"2021-06-21T00:00:00Z","doi":"10.1038/s41556-021-00700-2","page":"733–744","publication":"Nature Cell Biology","day":"21","year":"2021","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.)."},{"date_updated":"2023-08-10T13:56:31Z","department":[{"_id":"MaIb"}],"_id":"9626","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["2542-5293"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":20,"abstract":[{"text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.","lang":"eng"}],"oa_version":"None","scopus_import":"1","month":"06","intvolume":" 20","citation":{"apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. Elsevier. https://doi.org/10.1016/j.mtphys.2021.100452","ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 2021;20. doi:10.1016/j.mtphys.2021.100452","short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","ieee":"L. Su et al., “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” Materials Today Physics, vol. 20. Elsevier, 2021.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics, vol. 20, 100452, Elsevier, 2021, doi:10.1016/j.mtphys.2021.100452.","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” Materials Today Physics. Elsevier, 2021. https://doi.org/10.1016/j.mtphys.2021.100452."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Lizhong","last_name":"Su","full_name":"Su, Lizhong"},{"last_name":"Hong","full_name":"Hong, Tao","first_name":"Tao"},{"full_name":"Wang, Dongyang","last_name":"Wang","first_name":"Dongyang"},{"first_name":"Sining","full_name":"Wang, Sining","last_name":"Wang"},{"last_name":"Qin","full_name":"Qin, Bingchao","first_name":"Bingchao"},{"first_name":"Mengmeng","last_name":"Zhang","full_name":"Zhang, Mengmeng"},{"first_name":"Xiang","last_name":"Gao","full_name":"Gao, Xiang"},{"last_name":"Chang","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"article_processing_charge":"No","external_id":{"isi":["000703159600010"]},"title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","article_number":"100452","isi":1,"year":"2021","day":"03","publication":"Materials Today Physics","doi":"10.1016/j.mtphys.2021.100452","date_published":"2021-06-03T00:00:00Z","date_created":"2021-07-04T22:01:24Z","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","quality_controlled":"1","publisher":"Elsevier"},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"intvolume":" 12","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2021-12-17T11:34:50Z","file_size":3108845,"creator":"kschuh","date_created":"2021-12-17T11:34:50Z","file_name":"2021_NatureCommunications_Vandael.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10563","checksum":"6036a8cdae95e1707c2a04d54e325ff4","success":1}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/"}]},"issue":"1","volume":12,"_id":"9778","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-10T14:16:16Z","file_date_updated":"2021-12-17T11:34:50Z","department":[{"_id":"PeJo"}],"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Nature Communications","day":"18","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-08-06T07:22:55Z","doi":"10.1038/s41467-021-23153-5","date_published":"2021-05-18T00:00:00Z","article_number":"2912","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications, vol. 12, no. 1, 2912, Springer, 2021, doi:10.1038/s41467-021-23153-5.","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23153-5","apa":"Vandael, D. H., Okamoto, Y., & Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. Springer. https://doi.org/10.1038/s41467-021-23153-5","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” Nature Communications, vol. 12, no. 1. Springer, 2021.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” Nature Communications. Springer, 2021. https://doi.org/10.1038/s41467-021-23153-5.","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912."},"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","external_id":{"isi":["000655481800014"]},"article_processing_charge":"No","author":[{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael"},{"orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","first_name":"Yuji"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}]},{"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Long lived transients in gene regulation","author":[{"last_name":"Petrov","full_name":"Petrov, Tatjana","first_name":"Tatjana"},{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","full_name":"Igler, Claudia"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"external_id":{"isi":["000710180500002"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023."},"quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_published":"2021-06-04T00:00:00Z","doi":"10.1016/j.tcs.2021.05.023","date_created":"2021-07-11T22:01:18Z","page":"1-16","day":"04","publication":"Theoretical Computer Science","has_accepted_license":"1","isi":1,"year":"2021","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"9647","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2022-05-12T12:13:27Z","ddc":["004"],"date_updated":"2023-08-10T14:11:19Z","month":"06","intvolume":" 893","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"volume":893,"file":[{"date_created":"2022-05-12T12:13:27Z","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_updated":"2022-05-12T12:13:27Z","file_size":2566504,"creator":"dernst","checksum":"d3aef34cfb13e53bba4cf44d01680793","file_id":"11364","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-3975"]},"publication_status":"published"},{"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"article_processing_charge":"Yes","author":[{"full_name":"Muench, Nicole A.","last_name":"Muench","first_name":"Nicole A."},{"full_name":"Patel, Sonia","last_name":"Patel","first_name":"Sonia"},{"last_name":"Maes","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E"},{"full_name":"Donahue, Ryan J.","last_name":"Donahue","first_name":"Ryan J."},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593."},"article_number":"1593","date_created":"2021-08-01T22:01:22Z","doi":"10.3390/cells10071593","date_published":"2021-06-25T00:00:00Z","publication":"Cells","day":"25","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"MDPI","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","file_date_updated":"2021-08-04T14:01:30Z","department":[{"_id":"SaSi"}],"ddc":["570"],"date_updated":"2023-08-10T14:14:53Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9761","volume":10,"issue":"7","language":[{"iso":"eng"}],"file":[{"file_id":"9768","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","date_updated":"2021-08-04T14:01:30Z","file_size":4555611,"creator":"cziletti"}],"publication_status":"published","publication_identifier":{"eissn":["20734409"]},"intvolume":" 10","month":"06","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. "}]},{"day":"30","publication":"Neurobiology of Learning and Memory","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1016/j.nlm.2021.107486","date_published":"2021-06-30T00:00:00Z","date_created":"2021-07-11T22:01:16Z","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486.","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486","apa":"Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021."},"title":"The role of hippocampal mossy cells in novelty detection","author":[{"first_name":"Felipe","full_name":"Fredes, Felipe","last_name":"Fredes"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"article_processing_charge":"No","article_number":"107486","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"cziletti","file_size":1994793,"date_updated":"2021-07-19T13:46:06Z","file_name":"2021_NeurobLearnMemory_Fredes.pdf","date_created":"2021-07-19T13:46:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"8e8298a9e8c7df146ad23f32c2a63929","file_id":"9694"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10747427"],"eissn":["10959564"]},"publication_status":"published","volume":183,"ec_funded":1,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"month":"06","intvolume":" 183","scopus_import":"1","ddc":["610"],"date_updated":"2023-08-10T14:10:37Z","file_date_updated":"2021-07-19T13:46:06Z","department":[{"_id":"RySh"}],"_id":"9641","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"}},{"conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2021-06-26","location":"Online","start_date":"2021-06-20"},"type":"conference","status":"public","_id":"9646","department":[{"_id":"KrCh"}],"date_updated":"2023-08-10T14:14:08Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.14617"}],"scopus_import":"1","month":"06","abstract":[{"lang":"eng","text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude."}],"oa_version":"Preprint","ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"external_id":{"arxiv":["2011.14617"],"isi":["000723661700076"]},"article_processing_charge":"No","author":[{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"first_name":"Yican","full_name":"Sun, Yican","last_name":"Sun"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"title":"Quantitative analysis of assertion violations in probabilistic programs","citation":{"mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186.","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","page":"1171-1186","date_created":"2021-07-11T22:01:18Z","doi":"10.1145/3453483.3454102","date_published":"2021-06-01T00:00:00Z","year":"2021","isi":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","day":"01"},{"date_updated":"2023-08-10T14:13:39Z","department":[{"_id":"KrCh"}],"_id":"9645","conference":{"end_date":"2021-06-26","location":"Online","start_date":"2021-06-20","name":" PLDI: Programming Language Design and Implementation"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["9781450383912"]},"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"scopus_import":"1","month":"06","citation":{"apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787.","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000723661700050"]},"article_processing_charge":"No","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"},{"first_name":"Mohammad","full_name":"Mahdavi, Mohammad","last_name":"Mahdavi"}],"title":"Polynomial reachability witnesses via Stellensätze","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"year":"2021","isi":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","day":"01","page":"772-787","date_created":"2021-07-11T22:01:17Z","doi":"10.1145/3453483.3454076","date_published":"2021-06-01T00:00:00Z","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1"},{"publisher":"Public Library of Science","oa":1,"acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","doi":"10.1371/journal.pcbi.1009124","date_published":"2021-07-15T00:00:00Z","date_created":"2021-08-01T22:01:21Z","day":"15","publication":"PLoS Computational Biology","isi":1,"has_accepted_license":"1","year":"2021","article_number":"e1009124","title":"Ten simple rules to improve academic work- life balance","author":[{"last_name":"Bartlett","full_name":"Bartlett, Michael John","first_name":"Michael John"},{"last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N"},{"first_name":"Adriana","full_name":"Bankston, Adriana","last_name":"Bankston"},{"full_name":"Sarabipour, Sarvenaz","last_name":"Sarabipour","first_name":"Sarvenaz"}],"article_processing_charge":"Yes","external_id":{"pmid":["34264932"],"isi":["000677713500008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021.","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124."},"month":"07","intvolume":" 17","scopus_import":"1","pmid":1,"oa_version":"Published Version","volume":17,"issue":"7","file":[{"date_updated":"2021-08-05T12:06:49Z","file_size":693633,"creator":"cchlebak","date_created":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","file_id":"9771"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"],"eissn":["15537358"]},"publication_status":"published","status":"public","article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9759","department":[{"_id":"CaHe"}],"file_date_updated":"2021-08-05T12:06:49Z","ddc":["613"],"date_updated":"2023-08-10T14:16:46Z"},{"project":[{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850."},"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"author":[{"first_name":"Themistoklis","full_name":"Zisis, Themistoklis","last_name":"Zisis"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Miriam","last_name":"Balles","full_name":"Balles, Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","last_name":"Nemethova"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Lange","full_name":"Lange, Janina","first_name":"Janina"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Sixt","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","publication":"ACS Applied Materials and Interfaces","day":"04","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-08T22:01:28Z","date_published":"2021-08-04T00:00:00Z","doi":"10.1021/acsami.1c09850","page":"35545–35560","_id":"9822","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","ddc":["620","570"],"date_updated":"2023-08-10T14:22:48Z","file_date_updated":"2021-08-09T09:44:03Z","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"intvolume":" 13","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"9833","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-09T09:44:03Z","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","date_updated":"2021-08-09T09:44:03Z","file_size":7123293,"creator":"asandaue"}],"publication_status":"published","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"ec_funded":1,"volume":13,"issue":"30"},{"_id":"9819","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-10T14:25:08Z","ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2021-08-09T11:41:50Z","abstract":[{"lang":"eng","text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 40","month":"08","publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"language":[{"iso":"eng"}],"file":[{"creator":"asandaue","date_updated":"2021-08-09T11:41:50Z","file_size":49840741,"date_created":"2021-08-09T11:41:50Z","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","file_id":"9834","success":1}],"issue":"4","volume":40,"article_number":"44","citation":{"chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","ieee":"B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"author":[{"full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun","first_name":"B. R."},{"full_name":"Tewari, Ayush","last_name":"Tewari","first_name":"Ayush"},{"last_name":"Dib","full_name":"Dib, Abdallah","first_name":"Abdallah"},{"first_name":"Tim","full_name":"Weyrich, Tim","last_name":"Weyrich"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"first_name":"Louis","last_name":"Chevallier","full_name":"Chevallier, Louis"},{"last_name":"Elgharib","full_name":"Elgharib, Mohamed A.","first_name":"Mohamed A."},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"title":"PhotoApp: Photorealistic appearance editing of head portraits","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Graphics","day":"01","date_created":"2021-08-08T22:01:27Z","doi":"10.1145/3450626.3459765","date_published":"2021-08-01T00:00:00Z"},{"abstract":[{"text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 16","publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ae4df60eb62f4491278588548d0c1f93","file_id":"9835","creator":"asandaue","file_size":773921,"date_updated":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","date_created":"2021-08-09T11:52:14Z"}],"language":[{"iso":"eng"}],"volume":16,"issue":"7","_id":"9816","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-10T14:26:32Z","ddc":["610"],"file_date_updated":"2021-08-09T11:52:14Z","department":[{"_id":"NiBa"}],"acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"29","publication":"PLoS ONE","date_published":"2021-07-29T00:00:00Z","doi":"10.1371/journal.pone.0255267","date_created":"2021-08-08T22:01:26Z","article_number":"e0255267","citation":{"chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"},{"last_name":"Beiglböck","full_name":"Beiglböck, Mathias","first_name":"Mathias"},{"first_name":"Anna Nele","full_name":"Herdina, Anna Nele","last_name":"Herdina"},{"first_name":"Robert","full_name":"Strassl, Robert","last_name":"Strassl"},{"last_name":"Posch","full_name":"Posch, Martin","first_name":"Martin"}],"article_processing_charge":"Yes","external_id":{"pmid":["34324553"],"isi":["000685248200095"]},"title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program"},{"_id":"9821","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-10T14:21:42Z","ddc":["006"],"file_date_updated":"2021-08-09T09:25:41Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 16","publication_identifier":{"eissn":["19326203"]},"publication_status":"published","file":[{"file_size":2706919,"date_updated":"2021-08-09T09:25:41Z","creator":"asandaue","file_name":"2021_PLoSONE_Graff.pdf","date_created":"2021-08-09T09:25:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9832","checksum":"0277aa155d5db1febd2cb384768bba5f"}],"language":[{"iso":"eng"}],"issue":"7","volume":16,"article_number":"e0253851","citation":{"mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Grzegorz","full_name":"Graff, Grzegorz","last_name":"Graff"},{"first_name":"Beata","full_name":"Graff, Beata","last_name":"Graff"},{"last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","first_name":"Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","last_name":"Jablonski"},{"first_name":"Dariusz","full_name":"Gąsecki, Dariusz","last_name":"Gąsecki"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"article_processing_charge":"Yes","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"title":"Persistent homology as a new method of the assessment of heart rate variability","acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"PLoS ONE","doi":"10.1371/journal.pone.0253851","date_published":"2021-07-01T00:00:00Z","date_created":"2021-08-08T22:01:28Z"},{"article_number":"125","citation":{"ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., & Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459813","ieee":"A. Serrano et al., “The effect of shape and illumination on material perception: Model and applications,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021).","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Serrano","full_name":"Serrano, Ana","first_name":"Ana"},{"last_name":"Chen","full_name":"Chen, Bin","first_name":"Bin"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael"},{"first_name":"Hans Peter","full_name":"Seidel, Hans Peter","last_name":"Seidel"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"article_processing_charge":"No","external_id":{"isi":["000674930900090"]},"title":"The effect of shape and illumination on material perception: Model and applications","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"isi":1,"year":"2021","day":"01","publication":"ACM Transactions on Graphics","doi":"10.1145/3450626.3459813","date_published":"2021-08-01T00:00:00Z","date_created":"2021-08-08T22:01:28Z","_id":"9820","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-10T14:20:10Z","department":[{"_id":"BeBi"}],"abstract":[{"text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf"}],"month":"08","intvolume":" 40","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":40},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"month":"08","intvolume":" 40","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"},{"id":"9327","status":"public","relation":"software"}],"link":[{"url":"https://ist.ac.at/en/news/knitting-virtual-yarn/","relation":"press_release","description":"News on IST Webpage"}]},"issue":"4","volume":40,"ec_funded":1,"publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9818","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_updated":"2023-08-10T14:24:36Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459816","date_created":"2021-08-08T22:01:27Z","isi":1,"year":"2021","day":"01","publication":"ACM Transactions on Graphics","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"article_number":"168","author":[{"first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","full_name":"Sperl, Georg"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"external_id":{"isi":["000674930900132"]},"article_processing_charge":"Yes (in subscription journal)","title":"Mechanics-aware deformation of yarn pattern geometry","citation":{"ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","year":"2021","isi":1,"publication":"IEEE Transactions on Signal Processing","day":"09","page":"4039 - 4054","date_created":"2021-08-08T22:01:31Z","date_published":"2021-06-09T00:00:00Z","doi":"10.1109/TSP.2021.3087899","citation":{"ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000682123900002"],"arxiv":["2102.04832"]},"article_processing_charge":"No","author":[{"id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Mantas","full_name":"Gabrielaitis, Mantas","orcid":"0000-0002-7758-2016","last_name":"Gabrielaitis"}],"title":"Fast and accurate amplitude demodulation of wideband signals","abstract":[{"text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"scopus_import":"1","intvolume":" 69","month":"06","publication_status":"published","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"language":[{"iso":"eng"}],"volume":69,"_id":"9828","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-10T14:19:33Z","department":[{"_id":"GaTk"}]},{"file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"9328","checksum":"0324cb519273371708743f3282e7c081","file_size":802586232,"date_updated":"2021-04-16T14:15:12Z","creator":"gsperl","file_name":"MADYPG_extra_data.zip","date_created":"2021-04-16T14:15:12Z"},{"file_id":"9353","checksum":"4c224551adf852b136ec21a4e13f0c1b","access_level":"open_access","relation":"main_file","content_type":"application/gzip","date_created":"2021-04-26T09:33:44Z","file_name":"MADYPG.zip","creator":"pub-gitlab-bot","date_updated":"2021-04-26T09:33:44Z","file_size":64962865}],"year":"2021","has_accepted_license":"1","license":"https://opensource.org/licenses/MIT","date_created":"2021-04-16T14:26:19Z","related_material":{"record":[{"status":"public","id":"9818","relation":"used_for_analysis_in"}]},"doi":"10.15479/AT:ISTA:9327","date_published":"2021-05-01T00:00:00Z","gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573","gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","abstract":[{"text":"This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG","lang":"eng"}],"month":"05","oa":1,"publisher":"IST Austria","ddc":["005"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327","apa":"Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327","short":"G. Sperl, R. Narain, C. Wojtan, (2021).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9327.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327."},"date_updated":"2023-08-10T14:24:36Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"file_date_updated":"2021-04-26T09:33:44Z","title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","author":[{"full_name":"Sperl, Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"_id":"9327","status":"public","tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"type":"software"},{"acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review B","day":"01","year":"2021","isi":1,"date_created":"2021-08-04T15:05:32Z","date_published":"2021-07-01T00:00:00Z","doi":"10.1103/physrevb.104.024430","article_number":"024430","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.024430.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430.","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430.","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” Physical Review B, vol. 104, no. 2. American Physical Society, 2021.","short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 2021;104(2). doi:10.1103/physrevb.104.024430"},"title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","article_processing_charge":"No","external_id":{"arxiv":["2101.05173"],"isi":["000678780800003"]},"author":[{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alpern","full_name":"Alpern, Hen","first_name":"Hen"},{"full_name":"Paltiel, Yossi","last_name":"Paltiel","first_name":"Yossi"},{"full_name":"Millo, Oded","last_name":"Millo","first_name":"Oded"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data."}],"intvolume":" 104","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.05173"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"ec_funded":1,"volume":104,"issue":"2","_id":"9770","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-10T14:27:07Z","department":[{"_id":"MiLe"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","volume":886,"oa_version":"Submitted Version","abstract":[{"text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree.","lang":"eng"}],"month":"09","intvolume":" 886","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf"}],"date_updated":"2023-08-10T14:27:43Z","department":[{"_id":"DaAl"}],"_id":"9827","status":"public","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"article_type":"original","type":"journal_article","day":"13","publication":"Theoretical Computer Science","isi":1,"year":"2021","doi":"10.1016/j.tcs.2021.06.041","date_published":"2021-09-13T00:00:00Z","date_created":"2021-08-08T22:01:31Z","page":"27-48","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"B. 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Theoretical Computer Science. 886, 27–48.","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041."},"title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","author":[{"full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028","last_name":"Chatterjee","first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Walulya, Ivan","last_name":"Walulya","first_name":"Ivan"},{"first_name":"Philippas","full_name":"Tsigas, Philippas","last_name":"Tsigas"}],"article_processing_charge":"No","external_id":{"isi":["000694718900004"]}},{"citation":{"mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, vol. 118, no. 29. National Academy of Sciences, 2021.","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"author":[{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"first_name":"Deling","full_name":"Ruan, Deling","last_name":"Ruan"},{"last_name":"Nishimura","full_name":"Nishimura, Toshiro","first_name":"Toshiro"},{"last_name":"Sharma","full_name":"Sharma, Manoj K.","first_name":"Manoj K."},{"last_name":"Sharma","full_name":"Sharma, Rita","first_name":"Rita"},{"last_name":"Ye","full_name":"Ye, XinYi","first_name":"XinYi"},{"last_name":"Nguyen","full_name":"Nguyen, Nicholas D.","first_name":"Nicholas D."},{"first_name":"Sukhranjan","full_name":"Nijjar, Sukhranjan","last_name":"Nijjar"},{"first_name":"Pamela C.","full_name":"Ronald, Pamela C.","last_name":"Ronald"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","article_number":"e2104445118","year":"2021","isi":1,"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"16","date_created":"2021-08-10T19:30:41Z","doi":"10.1073/pnas.2104445118","date_published":"2021-07-16T00:00:00Z","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","date_updated":"2023-08-11T10:28:10Z","ddc":["580","570"],"file_date_updated":"2021-08-11T09:31:41Z","department":[{"_id":"DaZi"}],"_id":"9877","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"file":[{"file_size":1898360,"date_updated":"2021-08-11T09:31:41Z","creator":"asandaue","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","date_created":"2021-08-11T09:31:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9879","checksum":"19e84ad8c03c60222744ee8e16cd6998"}],"volume":118,"issue":"29","abstract":[{"text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 118","month":"07"},{"article_number":"4808","author":[{"last_name":"Raso","full_name":"Raso, Andrea","first_name":"Andrea"},{"full_name":"Dirkx, Ellen","last_name":"Dirkx","first_name":"Ellen"},{"full_name":"Sampaio-Pinto, Vasco","last_name":"Sampaio-Pinto","first_name":"Vasco"},{"last_name":"el Azzouzi","full_name":"el Azzouzi, Hamid","first_name":"Hamid"},{"first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","last_name":"Cubero"},{"first_name":"Daniel W.","full_name":"Sorensen, Daniel W.","last_name":"Sorensen"},{"first_name":"Lara","last_name":"Ottaviani","full_name":"Ottaviani, Lara"},{"full_name":"Olieslagers, Servé","last_name":"Olieslagers","first_name":"Servé"},{"last_name":"Huibers","full_name":"Huibers, Manon M.","first_name":"Manon M."},{"full_name":"de Weger, Roel","last_name":"de Weger","first_name":"Roel"},{"first_name":"Sailay","full_name":"Siddiqi, Sailay","last_name":"Siddiqi"},{"first_name":"Silvia","last_name":"Moimas","full_name":"Moimas, Silvia"},{"last_name":"Torrini","full_name":"Torrini, Consuelo","first_name":"Consuelo"},{"last_name":"Zentillin","full_name":"Zentillin, Lorena","first_name":"Lorena"},{"last_name":"Braga","full_name":"Braga, Luca","first_name":"Luca"},{"first_name":"Diana S.","full_name":"Nascimento, Diana S.","last_name":"Nascimento"},{"first_name":"Paula A.","last_name":"da Costa Martins","full_name":"da Costa Martins, Paula A."},{"first_name":"Jop H.","last_name":"van Berlo","full_name":"van Berlo, Jop H."},{"full_name":"Zacchigna, Serena","last_name":"Zacchigna","first_name":"Serena"},{"full_name":"Giacca, Mauro","last_name":"Giacca","first_name":"Mauro"},{"full_name":"De Windt, Leon J.","last_name":"De Windt","first_name":"Leon J."}],"article_processing_charge":"Yes","external_id":{"pmid":["34376683"],"isi":["000683910200042"]},"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","citation":{"mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications, vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4.","ieee":"A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications, vol. 12. Springer Nature, 2021.","short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4.","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","genbank":["GSE178867"],"oa":1,"acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","date_published":"2021-08-10T00:00:00Z","doi":"10.1038/s41467-021-25211-4","date_created":"2021-08-10T11:49:20Z","isi":1,"has_accepted_license":"1","year":"2021","day":"10","publication":"Nature Communications","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9874","file_date_updated":"2021-08-10T12:29:59Z","department":[{"_id":"SaSi"}],"date_updated":"2023-08-11T10:27:03Z","ddc":["610","570"],"scopus_import":"1","month":"08","intvolume":" 12","abstract":[{"text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":12,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-32785-0"}]},"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"date_updated":"2021-08-10T12:29:59Z","file_size":4364333,"creator":"asandaue","date_created":"2021-08-10T12:29:59Z","file_name":"2021_NatureCommunications_Raso.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"48d8562e8229e4282f3f354b329722c5","file_id":"9876","success":1}],"language":[{"iso":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"SciPost","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","date_created":"2021-08-04T15:00:55Z","doi":"10.21468/scipostphys.11.1.008","date_published":"2021-07-13T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"SciPost Physics","day":"13","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"article_number":"008","article_processing_charge":"Yes","external_id":{"isi":["000680039500013"],"arxiv":["2101.10958"]},"author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"first_name":"Hans-Werner","last_name":"Hammer","full_name":"Hammer, Hans-Werner"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"title":"Impurities in a one-dimensional Bose gas: The flow equation approach","citation":{"chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021, doi:10.21468/scipostphys.11.1.008.","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost, 2021.","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.1.008","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 11","month":"07","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"oa_version":"Published Version","ec_funded":1,"volume":11,"issue":"1","publication_status":"published","publication_identifier":{"eissn":["2542-4653"]},"language":[{"iso":"eng"}],"file":[{"file_id":"9875","checksum":"eaa847346b1a023d97bbb291779610ed","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-10T11:44:59Z","file_name":"2021_SciPostPhysics_Brauneis.pdf","creator":"asandaue","date_updated":"2021-08-10T11:44:59Z","file_size":1085300}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"9769","department":[{"_id":"MiLe"}],"file_date_updated":"2021-08-10T11:44:59Z","date_updated":"2023-08-11T10:25:44Z","ddc":["530"]},{"publication":"eLife","day":"28","year":"2021","isi":1,"date_created":"2021-07-28T13:36:57Z","doi":"10.7554/elife.68876","date_published":"2021-07-28T00:00:00Z","acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021.","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876.","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876."},"title":"High potency of sequential therapy with only beta-lactam antibiotics","article_processing_charge":"No","external_id":{"pmid":["34318749"],"isi":["000692027800001"]},"author":[{"last_name":"Batra","full_name":"Batra, Aditi","first_name":"Aditi"},{"first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","orcid":"0000-0001-9480-5261","full_name":"Römhild, Roderich","last_name":"Römhild"},{"full_name":"Rousseau, Emilie","last_name":"Rousseau","first_name":"Emilie"},{"full_name":"Franzenburg, Sören","last_name":"Franzenburg","first_name":"Sören"},{"last_name":"Niemann","full_name":"Niemann, Stefan","first_name":"Stefan"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"}],"article_number":"e68876","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"volume":10,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"intvolume":" 10","month":"07","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-11T10:26:29Z","department":[{"_id":"CaGu"}],"_id":"9746","status":"public","type":"journal_article","article_type":"original"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","page":"56-73","date_created":"2021-08-15T22:01:29Z","date_published":"2021-08-11T00:00:00Z","doi":"10.1111/jmi.13041","year":"2021","isi":1,"publication":"Journal of Microscopy","day":"11","article_processing_charge":"Yes","external_id":{"isi":["000683702700001"]},"author":[{"full_name":"Nelson, Glyn","last_name":"Nelson","first_name":"Glyn"},{"last_name":"Boehm","full_name":"Boehm, Ulrike","first_name":"Ulrike"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"last_name":"Bajcsy","full_name":"Bajcsy, Peter","first_name":"Peter"},{"first_name":"Johanna","full_name":"Bischof, Johanna","last_name":"Bischof"},{"last_name":"Brown","full_name":"Brown, Claire M.","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","last_name":"Dauphin","first_name":"Aurélien"},{"first_name":"Ian M.","full_name":"Dobbie, Ian M.","last_name":"Dobbie"},{"last_name":"Eriksson","full_name":"Eriksson, John E.","first_name":"John E."},{"last_name":"Faklaris","full_name":"Faklaris, Orestis","first_name":"Orestis"},{"first_name":"Julia","last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia"},{"last_name":"Ferrand","full_name":"Ferrand, Alexia","first_name":"Alexia"},{"last_name":"Gelman","full_name":"Gelman, Laurent","first_name":"Laurent"},{"first_name":"Ali","last_name":"Gheisari","full_name":"Gheisari, Ali"},{"first_name":"Hella","full_name":"Hartmann, Hella","last_name":"Hartmann"},{"first_name":"Christian","full_name":"Kukat, Christian","last_name":"Kukat"},{"full_name":"Laude, Alex","last_name":"Laude","first_name":"Alex"},{"full_name":"Mitkovski, Miso","last_name":"Mitkovski","first_name":"Miso"},{"last_name":"Munck","full_name":"Munck, Sebastian","first_name":"Sebastian"},{"first_name":"Alison J.","last_name":"North","full_name":"North, Alison J."},{"first_name":"Tobias M.","last_name":"Rasse","full_name":"Rasse, Tobias M."},{"last_name":"Resch-Genger","full_name":"Resch-Genger, Ute","first_name":"Ute"},{"full_name":"Schuetz, Lucas C.","last_name":"Schuetz","first_name":"Lucas C."},{"first_name":"Arne","full_name":"Seitz, Arne","last_name":"Seitz"},{"last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina"},{"full_name":"Swedlow, Jason R.","last_name":"Swedlow","first_name":"Jason R."},{"first_name":"Ioannis","full_name":"Alexopoulos, Ioannis","last_name":"Alexopoulos"},{"first_name":"Karin","last_name":"Aumayr","full_name":"Aumayr, Karin"},{"last_name":"Avilov","full_name":"Avilov, Sergiy","first_name":"Sergiy"},{"last_name":"Bakker","full_name":"Bakker, Gert Jan","first_name":"Gert Jan"},{"full_name":"Bammann, Rodrigo R.","last_name":"Bammann","first_name":"Rodrigo R."},{"first_name":"Andrea","last_name":"Bassi","full_name":"Bassi, Andrea"},{"full_name":"Beckert, Hannes","last_name":"Beckert","first_name":"Hannes"},{"first_name":"Sebastian","full_name":"Beer, Sebastian","last_name":"Beer"},{"first_name":"Yury","last_name":"Belyaev","full_name":"Belyaev, Yury"},{"last_name":"Bierwagen","full_name":"Bierwagen, Jakob","first_name":"Jakob"},{"first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A.","last_name":"Birngruber"},{"first_name":"Manel","last_name":"Bosch","full_name":"Bosch, Manel"},{"full_name":"Breitlow, Juergen","last_name":"Breitlow","first_name":"Juergen"},{"full_name":"Cameron, Lisa A.","last_name":"Cameron","first_name":"Lisa A."},{"first_name":"Joe","last_name":"Chalfoun","full_name":"Chalfoun, Joe"},{"last_name":"Chambers","full_name":"Chambers, James J.","first_name":"James J."},{"first_name":"Chieh Li","last_name":"Chen","full_name":"Chen, Chieh Li"},{"first_name":"Eduardo","last_name":"Conde-Sousa","full_name":"Conde-Sousa, Eduardo"},{"last_name":"Corbett","full_name":"Corbett, Alexander D.","first_name":"Alexander 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Gerhard A."},{"full_name":"Itano, Michelle S.","last_name":"Itano","first_name":"Michelle S."},{"full_name":"Jaffe, Claudia B.","last_name":"Jaffe","first_name":"Claudia B."},{"first_name":"Helena K.","last_name":"Jambor","full_name":"Jambor, Helena K."},{"first_name":"Stuart C.","last_name":"Jarvis","full_name":"Jarvis, Stuart C."},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler","first_name":"David"},{"full_name":"Kirchner, Marcel","last_name":"Kirchner","first_name":"Marcel"},{"first_name":"Norio","last_name":"Kobayashi","full_name":"Kobayashi, Norio"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Susanne","full_name":"Kunis, Susanne","last_name":"Kunis"},{"last_name":"Lacoste","full_name":"Lacoste, Judith","first_name":"Judith"},{"first_name":"Marco","last_name":"Marcello","full_name":"Marcello, Marco"},{"last_name":"Martins","full_name":"Martins, Gabriel G.","first_name":"Gabriel G."},{"first_name":"Daniel J.","last_name":"Metcalf","full_name":"Metcalf, Daniel J."},{"last_name":"Mitchell","full_name":"Mitchell, Claire A.","first_name":"Claire A."},{"first_name":"Joshua","full_name":"Moore, Joshua","last_name":"Moore"},{"first_name":"Tobias","last_name":"Mueller","full_name":"Mueller, Tobias"},{"first_name":"Michael S.","full_name":"Nelson, Michael S.","last_name":"Nelson"},{"full_name":"Ogg, Stephen","last_name":"Ogg","first_name":"Stephen"},{"first_name":"Shuichi","full_name":"Onami, Shuichi","last_name":"Onami"},{"last_name":"Palmer","full_name":"Palmer, Alexandra L.","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine"},{"last_name":"Pimentel","full_name":"Pimentel, Jaime A.","first_name":"Jaime A."},{"full_name":"Plantard, Laure","last_name":"Plantard","first_name":"Laure"},{"first_name":"Santosh","full_name":"Podder, Santosh","last_name":"Podder"},{"first_name":"Elton","last_name":"Rexhepaj","full_name":"Rexhepaj, Elton"},{"first_name":"Arnaud","full_name":"Royon, Arnaud","last_name":"Royon"},{"last_name":"Saari","full_name":"Saari, Markku A.","first_name":"Markku A."},{"full_name":"Schapman, Damien","last_name":"Schapman","first_name":"Damien"},{"last_name":"Schoonderwoert","full_name":"Schoonderwoert, Vincent","first_name":"Vincent"},{"full_name":"Schroth-Diez, Britta","last_name":"Schroth-Diez","first_name":"Britta"},{"last_name":"Schwartz","full_name":"Schwartz, Stanley","first_name":"Stanley"},{"last_name":"Shaw","full_name":"Shaw, Michael","first_name":"Michael"},{"first_name":"Martin","full_name":"Spitaler, Martin","last_name":"Spitaler"},{"last_name":"Stoeckl","full_name":"Stoeckl, Martin T.","first_name":"Martin T."},{"full_name":"Sudar, Damir","last_name":"Sudar","first_name":"Damir"},{"first_name":"Jeremie","last_name":"Teillon","full_name":"Teillon, Jeremie"},{"last_name":"Terjung","full_name":"Terjung, Stefan","first_name":"Stefan"},{"first_name":"Roland","full_name":"Thuenauer, Roland","last_name":"Thuenauer"},{"first_name":"Christian D.","full_name":"Wilms, Christian D.","last_name":"Wilms"},{"first_name":"Graham D.","last_name":"Wright","full_name":"Wright, Graham D."},{"first_name":"Roland","last_name":"Nitschke","full_name":"Nitschke, Roland"}],"title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","citation":{"mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"scopus_import":"1","intvolume":" 284","month":"08","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":284,"publication_status":"published","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9911","department":[{"_id":"Bio"}],"date_updated":"2023-08-11T10:30:40Z"},{"ddc":["570"],"date_updated":"2023-08-11T10:34:13Z","department":[{"_id":"SiHi"}],"file_date_updated":"2021-08-16T09:29:17Z","_id":"9906","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"creator":"asandaue","date_updated":"2021-08-16T09:29:17Z","file_size":2646018,"date_created":"2021-08-16T09:29:17Z","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9922","checksum":"be7f0042607ca60549cb27513c19c6af","success":1}],"publication_status":"published","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"volume":22,"issue":"16","oa_version":"Published Version","abstract":[{"text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways.","lang":"eng"}],"intvolume":" 22","month":"08","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22168385.","ieee":"I. Yotova et al., “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” International Journal of Molecular Sciences, vol. 22, no. 16. MDPI, 2021.","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 2021;22(16). doi:10.3390/ijms22168385","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22168385","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” International Journal of Molecular Sciences, vol. 22, no. 16, 8385, MDPI, 2021, doi:10.3390/ijms22168385."},"title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","article_processing_charge":"Yes","external_id":{"isi":["000689147400001"]},"author":[{"first_name":"Iveta","full_name":"Yotova, Iveta","last_name":"Yotova"},{"last_name":"Hudson","full_name":"Hudson, Quanah J.","first_name":"Quanah J."},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"first_name":"Katharina","full_name":"Proestling, Katharina","last_name":"Proestling"},{"first_name":"Isabella","last_name":"Haslinger","full_name":"Haslinger, Isabella"},{"first_name":"Lorenz","last_name":"Kuessel","full_name":"Kuessel, Lorenz"},{"full_name":"Perricos, Alexandra","last_name":"Perricos","first_name":"Alexandra"},{"last_name":"Husslein","full_name":"Husslein, Heinrich","first_name":"Heinrich"},{"first_name":"René","last_name":"Wenzl","full_name":"Wenzl, René"}],"article_number":"8385","publication":"International Journal of Molecular Sciences","day":"04","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-15T22:01:27Z","date_published":"2021-08-04T00:00:00Z","doi":"10.3390/ijms22168385","acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","oa":1,"quality_controlled":"1","publisher":"MDPI"},{"author":[{"first_name":"Sergei A.","last_name":"Slavskii","full_name":"Slavskii, Sergei A."},{"first_name":"Ivan A.","full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov"},{"first_name":"Tatiana I.","full_name":"Shashkova, Tatiana I.","last_name":"Shashkova"},{"full_name":"Bazykin, Georgii A.","last_name":"Bazykin","first_name":"Georgii A."},{"first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I.","last_name":"Axenovich"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Aulchenko","full_name":"Aulchenko, Yurii S.","first_name":"Yurii S."}],"external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"article_processing_charge":"Yes (in subscription journal)","title":"The limits of normal approximation for adult height","citation":{"mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:10.1038/s41431-021-00836-7.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-021-00836-7","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091. doi:10.1038/s41431-021-00836-7","ieee":"S. A. Slavskii et al., “The limits of normal approximation for adult height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” European Journal of Human Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"1082-1091","doi":"10.1038/s41431-021-00836-7","date_published":"2021-07-01T00:00:00Z","date_created":"2021-08-15T22:01:28Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"European Journal of Human Genetics","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","file_date_updated":"2021-08-16T09:14:36Z","department":[{"_id":"FyKo"}],"date_updated":"2023-08-11T10:33:42Z","ddc":["576"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9910","issue":"7","volume":29,"ec_funded":1,"publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a676d76f91b0dbe0504c63e469129c2a","file_id":"9921","file_size":1079395,"date_updated":"2021-08-16T09:14:36Z","creator":"asandaue","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","date_created":"2021-08-16T09:14:36Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 29","abstract":[{"text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"publication":"Annales Henri Poincaré ","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-08-15T22:01:29Z","doi":"10.1007/s00023-021-01085-6","date_published":"2021-12-01T00:00:00Z","page":"4205–4269","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré , vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:10.1007/s00023-021-01085-6.","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” Annales Henri Poincaré , vol. 22. Springer Nature, pp. 4205–4269, 2021.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré 22 (2021) 4205–4269.","apa":"Erdös, L., Krüger, T. H., & Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . Springer Nature. https://doi.org/10.1007/s00023-021-01085-6","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 2021;22:4205–4269. doi:10.1007/s00023-021-01085-6","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” Annales Henri Poincaré . Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01085-6.","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269."},"title":"Scattering in quantum dots via noncommutative rational functions","external_id":{"arxiv":["1911.05112"],"isi":["000681531500001"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"},{"full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","last_name":"Nemish","first_name":"Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"language":[{"iso":"eng"}],"file":[{"date_created":"2022-05-12T12:50:27Z","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","date_updated":"2022-05-12T12:50:27Z","file_size":1162454,"creator":"dernst","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","file_id":"11365","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"ec_funded":1,"volume":22,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries."}],"intvolume":" 22","month":"12","scopus_import":"1","ddc":["510"],"date_updated":"2023-08-11T10:31:48Z","file_date_updated":"2022-05-12T12:50:27Z","department":[{"_id":"LaEr"}],"_id":"9912","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"abstract":[{"text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 62","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"publication_status":"published","file":[{"file_id":"10188","checksum":"d035be2b894c4d50d90ac5ce252e27cd","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-27T12:57:06Z","file_name":"2021_JMathPhy_Lauritsen.pdf","creator":"cziletti","date_updated":"2021-10-27T12:57:06Z","file_size":4352640}],"language":[{"iso":"eng"}],"issue":"8","volume":62,"_id":"9891","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"date_updated":"2023-08-11T10:29:48Z","ddc":["530"],"file_date_updated":"2021-10-27T12:57:06Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Journal of Mathematical Physics","doi":"10.1063/5.0053494","date_published":"2021-08-01T00:00:00Z","date_created":"2021-08-12T07:08:36Z","article_number":"083305","citation":{"mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:10.1063/5.0053494.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0053494","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 2021;62(8). doi:10.1063/5.0053494","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” Journal of Mathematical Physics, vol. 62, no. 8. AIP Publishing, 2021.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0053494.","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"}],"external_id":{"isi":["000683960800003"],"arxiv":["2103.07975"]},"article_processing_charge":"No","title":"Floating Wigner crystal and periodic jellium configurations"},{"month":"07","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition."}],"issue":"8","volume":12,"file":[{"file_size":1340305,"date_updated":"2021-08-16T09:02:40Z","creator":"asandaue","file_name":"2021_Genes_Zeng.pdf","date_created":"2021-08-16T09:02:40Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9919","checksum":"3d99535618cf9a5b14d264408fa52e97"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20734425"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9909","department":[{"_id":"JiFr"}],"file_date_updated":"2021-08-16T09:02:40Z","ddc":["580","570"],"date_updated":"2023-08-11T10:32:21Z","publisher":"MDPI","quality_controlled":"1","oa":1,"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","doi":"10.3390/genes12081141","date_published":"2021-07-27T00:00:00Z","date_created":"2021-08-15T22:01:28Z","day":"27","publication":"Genes","has_accepted_license":"1","isi":1,"year":"2021","article_number":"1141","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","author":[{"first_name":"Yinwei","last_name":"Zeng","full_name":"Zeng, Yinwei"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"first_name":"Hoang Khai","last_name":"Trinh","full_name":"Trinh, Hoang Khai"},{"first_name":"Thomas","last_name":"Heugebaert","full_name":"Heugebaert, Thomas"},{"full_name":"Stevens, Christian V.","last_name":"Stevens","first_name":"Christian V."},{"first_name":"Irene","last_name":"Garcia-Maquilon","full_name":"Garcia-Maquilon, Irene"},{"last_name":"Rodriguez","full_name":"Rodriguez, Pedro L.","first_name":"Pedro L."},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"}],"external_id":{"isi":["000690558000001"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021, doi:10.3390/genes12081141.","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141."}},{"_id":"9907","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-08-11T10:34:44Z","department":[{"_id":"MaLo"}],"file_date_updated":"2021-08-16T09:35:56Z","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"08","intvolume":" 22","scopus_import":"1","file":[{"creator":"asandaue","date_updated":"2021-08-16T09:35:56Z","file_size":6132410,"date_created":"2021-08-16T09:35:56Z","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9923","checksum":"a4bc06e9a2c803ceff5a91f10b174054","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"publication_status":"published","volume":22,"issue":"15","ec_funded":1,"article_number":"8350","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22158350.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” International Journal of Molecular Sciences, vol. 22, no. 15. MDPI, 2021.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 2021;22(15). doi:10.3390/ijms22158350","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., & Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22158350","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” International Journal of Molecular Sciences, vol. 22, no. 15, 8350, MDPI, 2021, doi:10.3390/ijms22158350."},"title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","author":[{"first_name":"Naďa","last_name":"Labajová","full_name":"Labajová, Naďa"},{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miroslav","full_name":"Jurásek, Miroslav","last_name":"Jurásek"},{"first_name":"Robert","last_name":"Vácha","full_name":"Vácha, Robert"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"},{"first_name":"Imrich","full_name":"Barák, Imrich","last_name":"Barák"}],"article_processing_charge":"Yes","external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","quality_controlled":"1","publisher":"MDPI","oa":1,"day":"01","publication":"International Journal of Molecular Sciences","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-08-01T00:00:00Z","doi":"10.3390/ijms22158350","date_created":"2021-08-15T22:01:27Z"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","date_created":"2021-08-15T22:01:26Z","doi":"10.1038/s41598-021-95025-3","date_published":"2021-07-30T00:00:00Z","publication":"Scientific Reports","day":"30","year":"2021","has_accepted_license":"1","isi":1,"project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"article_number":"15729","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","article_processing_charge":"Yes","external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon","full_name":"Rella, Simon","last_name":"Rella"},{"first_name":"Yuliya A.","full_name":"Kulikova, Yuliya A.","last_name":"Kulikova"},{"first_name":"Emmanouil T.","last_name":"Dermitzakis","full_name":"Dermitzakis, Emmanouil T."},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-95025-3.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729."},"intvolume":" 11","month":"07","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"ec_funded":1,"volume":11,"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/"}]},"issue":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"ac86892ed17e6724c7251844da5cef5c","file_id":"9927","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_ScientificReports_Rella.pdf","date_created":"2021-08-16T11:36:49Z","file_size":3432001,"date_updated":"2021-08-16T11:36:49Z","creator":"asandaue"}],"publication_status":"published","publication_identifier":{"eissn":["20452322"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"9905","department":[{"_id":"FyKo"}],"file_date_updated":"2021-08-16T11:36:49Z","ddc":["570","610"],"date_updated":"2023-08-11T10:42:58Z"},{"article_number":"060602","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.060602.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” Physical Review Letters, vol. 127, no. 6. American Physical Society, 2021.","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 2021;127(6). doi:10.1103/physrevlett.127.060602","apa":"Karle, V., Serbyn, M., & Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.060602","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” Physical Review Letters, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:10.1103/physrevlett.127.060602."},"title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","last_name":"Karle","full_name":"Karle, Volker","orcid":"0000-0002-6963-0129"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis"}],"external_id":{"arxiv":["2102.13633"],"isi":["000684276000002"]},"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"06","publication":"Physical Review Letters","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1103/physrevlett.127.060602","date_published":"2021-08-06T00:00:00Z","date_created":"2021-08-13T09:27:39Z","_id":"9903","status":"public","article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["539"],"date_updated":"2023-08-11T10:43:27Z","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"file_date_updated":"2021-08-13T09:28:08Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures."}],"month":"08","intvolume":" 127","file":[{"creator":"mserbyn","date_updated":"2021-08-13T09:28:08Z","file_size":5064231,"date_created":"2021-08-13T09:28:08Z","file_name":"PhysRevLett.127.060602_SOM.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9904","checksum":"51218f302dcef99d90d1209809fcc874","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","volume":127,"issue":"6","ec_funded":1},{"article_number":"jcs255018","author":[{"first_name":"Agathe","full_name":"Chaigne, Agathe","last_name":"Chaigne"},{"last_name":"Smith","full_name":"Smith, Matthew B.","first_name":"Matthew B."},{"first_name":"R. L.","full_name":"Cavestany, R. L.","last_name":"Cavestany"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000681395800008"]},"title":"Three-dimensional geometry controls division symmetry in stem cell colonies","citation":{"mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:10.1242/jcs.255018.","short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” Journal of Cell Science, vol. 134, no. 14. The Company of Biologists, 2021.","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 2021;134(14). doi:10.1242/jcs.255018","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.255018","chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” Journal of Cell Science. The Company of Biologists, 2021. https://doi.org/10.1242/jcs.255018.","ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"The Company of Biologists","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","date_published":"2021-07-01T00:00:00Z","doi":"10.1242/jcs.255018","date_created":"2021-08-22T22:01:20Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Journal of Cell Science","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9952","file_date_updated":"2021-08-23T07:32:20Z","department":[{"_id":"EdHa"}],"date_updated":"2023-08-11T10:55:36Z","ddc":["570"],"scopus_import":"1","month":"07","intvolume":" 134","abstract":[{"lang":"eng","text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry."}],"oa_version":"Published Version","volume":134,"issue":"14","publication_identifier":{"eissn":["14779137"],"issn":["00219533"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"f086f9d7cb63b2474c01921cb060c513","file_id":"9954","creator":"asandaue","file_size":8651724,"date_updated":"2021-08-23T07:32:20Z","file_name":"2021_JournalOfCellScience_Chaigne.pdf","date_created":"2021-08-23T07:32:20Z"}],"language":[{"iso":"eng"}]},{"citation":{"mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes, vol. 12, no. 8, 1136, MDPI, 2021, doi:10.3390/genes12081136.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” Genes, vol. 12, no. 8. MDPI, 2021.","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., & Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. MDPI. https://doi.org/10.3390/genes12081136","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 2021;12(8). doi:10.3390/genes12081136","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081136.","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"isi":["000690475900001"]},"author":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Stéphanie","last_name":"Bertrand","full_name":"Bertrand, Stéphanie"},{"full_name":"Escriva, Hector","last_name":"Escriva","first_name":"Hector"}],"title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","article_number":"1136","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"Genes","day":"01","date_created":"2021-08-15T22:01:27Z","doi":"10.3390/genes12081136","date_published":"2021-08-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"MDPI","date_updated":"2023-08-11T10:42:32Z","ddc":["570"],"department":[{"_id":"BeVi"}],"file_date_updated":"2021-08-16T09:49:35Z","_id":"9908","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"review","status":"public","publication_status":"published","publication_identifier":{"eissn":["20734425"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9926","checksum":"744e60e56d290a96da3c91a9779f886f","success":1,"creator":"asandaue","date_updated":"2021-08-16T09:49:35Z","file_size":2297655,"date_created":"2021-08-16T09:49:35Z","file_name":"2021_Genes_Picard.pdf"}],"ec_funded":1,"issue":"8","volume":12,"abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"08"},{"page":"10743–10747","date_created":"2021-08-08T22:01:31Z","date_published":"2021-07-06T00:00:00Z","doi":"10.1021/acsnano.1c03276","year":"2021","isi":1,"publication":"ACS Nano","day":"06","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","external_id":{"pmid":["34228432"],"isi":["000679406500002"]},"article_processing_charge":"No","author":[{"last_name":"Baranov","full_name":"Baranov, Dmitry","first_name":"Dmitry"},{"first_name":"Tara","last_name":"Šverko","full_name":"Šverko, Tara"},{"first_name":"Taylor","last_name":"Moot","full_name":"Moot, Taylor"},{"last_name":"Keller","full_name":"Keller, Helena R.","first_name":"Helena R."},{"full_name":"Klein, Megan D.","last_name":"Klein","first_name":"Megan D."},{"first_name":"E. K.","last_name":"Vishnu","full_name":"Vishnu, E. K."},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Shulenberger","full_name":"Shulenberger, Katherine E.","first_name":"Katherine E."}],"title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","citation":{"mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:10.1021/acsnano.1c03276.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","ieee":"D. Baranov et al., “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” ACS Nano, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 2021;15(7):10743–10747. doi:10.1021/acsnano.1c03276","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.1c03276","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” ACS Nano. American Chemical Society, 2021. https://doi.org/10.1021/acsnano.1c03276.","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","volume":15,"publication_status":"published","publication_identifier":{"issn":["19360851"],"eissn":["1936086X"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"07","abstract":[{"text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"MaIb"}],"date_updated":"2023-08-11T10:55:08Z","type":"journal_article","article_type":"original","status":"public","_id":"9829"}]