[{"type":"journal_article","abstract":[{"lang":"eng","text":"The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups."}],"status":"public","ddc":["618"],"title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","intvolume":" 11","_id":"10069","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"cchlebak","file_size":6970368,"content_type":"application/pdf","file_name":"2021_ScientificReports_Robinson.pdf","access_level":"open_access","date_created":"2021-10-05T14:56:48Z","date_updated":"2021-10-05T14:56:48Z","success":1,"checksum":"f002ec22f609f58e1263b79e7f79601e","file_id":"10091","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"28","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Scientific Reports","citation":{"chicago":"Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-98411-z.","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","mla":"Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” Scientific Reports, vol. 11, 19238, Springer Nature, 2021, doi:10.1038/s41598-021-98411-z.","ieee":"M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” Scientific Reports, vol. 11. Springer Nature, 2021.","apa":"Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., & Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-98411-z","ista":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238.","ama":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 2021;11. doi:10.1038/s41598-021-98411-z"},"date_published":"2021-09-28T00:00:00Z","article_number":"19238","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2021-10-05T14:56:48Z","publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors for the computerized obstetrical data.","year":"2021","pmid":1,"date_created":"2021-10-03T22:01:21Z","date_updated":"2023-08-14T07:05:15Z","volume":11,"author":[{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"full_name":"Stojanov, Miloš","first_name":"Miloš","last_name":"Stojanov"},{"first_name":"Sabine","last_name":"Blum","full_name":"Blum, Sabine"},{"full_name":"Baud, David","last_name":"Baud","first_name":"David"}],"month":"09","publication_identifier":{"eissn":["2045-2322"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34584125"],"isi":["000701575500083"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-98411-z"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1038/s41586-021-03938-w","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000706977400002"],"arxiv":["2104.00653"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.00653"}],"ec_funded":1,"date_updated":"2023-08-14T07:04:06Z","date_created":"2021-09-19T22:01:25Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-021-04181-z"}]},"author":[{"first_name":"Haoxin","last_name":"Zhou","full_name":"Zhou, Haoxin"},{"full_name":"Xie, Tian","last_name":"Xie","first_name":"Tian"},{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"last_name":"Ehrets","first_name":"James R.","full_name":"Ehrets, James R."},{"full_name":"Spanton, Eric M.","first_name":"Eric M.","last_name":"Spanton"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"first_name":"Erez","last_name":"Berg","full_name":"Berg, Erez"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."}],"publisher":"Springer Nature","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"The authors acknowledge discussions with A. Macdonald, L. Fu, F. Wang and M. Zaletel. AFY acknowledges support of the National Science Foundation under DMR1654186, and the Gordon and Betty Moore Foundation under award GBMF9471. The authors acknowledge the use of the research facilities within the California NanoSystems Institute, supported by the University of California, Santa Barbara and the University of California, Office of the President.\r\nK.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, Grant Number JPMXP0112101001 and JSPS KAKENHI, Grant Number JP20H00354. EB and TH were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement\r\nNo. 754411.\r\n","year":"2021","article_processing_charge":"No","day":"01","keyword":["condensed matter - mesoscale and nanoscale physics","condensed matter - strongly correlated electrons","multidisciplinary"],"scopus_import":"1","date_published":"2021-09-01T00:00:00Z","article_type":"original","citation":{"mla":"Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w.","short":"H. Zhou, T. Xie, A. Ghazaryan, T. Holder, J.R. Ehrets, E.M. Spanton, T. Taniguchi, K. Watanabe, E. Berg, M. Serbyn, A.F. Young, Nature (2021).","chicago":"Zhou, Haoxin, Tian Xie, Areg Ghazaryan, Tobias Holder, James R. Ehrets, Eric M. Spanton, Takashi Taniguchi, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03938-w.","ama":"Zhou H, Xie T, Ghazaryan A, et al. Half and quarter metals in rhombohedral trilayer graphene. Nature. 2021. doi:10.1038/s41586-021-03938-w","ista":"Zhou H, Xie T, Ghazaryan A, Holder T, Ehrets JR, Spanton EM, Taniguchi T, Watanabe K, Berg E, Serbyn M, Young AF. 2021. Half and quarter metals in rhombohedral trilayer graphene. Nature.","apa":"Zhou, H., Xie, T., Ghazaryan, A., Holder, T., Ehrets, J. R., Spanton, E. M., … Young, A. F. (2021). Half and quarter metals in rhombohedral trilayer graphene. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03938-w","ieee":"H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,” Nature. Springer Nature, 2021."},"publication":"Nature","abstract":[{"lang":"eng","text":"Ferromagnetism is most common in transition metal compounds but may also arise in low-density two-dimensional electron systems, with signatures observed in silicon, III-V semiconductor systems, and graphene moiré heterostructures. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive the spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors. Using capacitance measurements on graphite-gated van der Waals heterostructures, we find a cascade of density- and electronic displacement field tuned phase transitions marked by negative electronic compressibility. The transitions define the boundaries between phases where quantum oscillations have either four-fold, two-fold, or one-fold degeneracy, associated with a spin and valley degenerate normal metal, spin-polarized `half-metal', and spin and valley polarized `quarter metal', respectively. For electron doping, the salient features are well captured by a phenomenological Stoner model with a valley-anisotropic Hund's coupling, likely arising from interactions at the lattice scale. For hole filling, we observe a richer phase diagram featuring a delicate interplay of broken symmetries and transitions in the Fermi surface topology. Finally, by rotational alignment of a hexagonal boron nitride substrate to induce a moiré superlattice, we find that the superlattice perturbs the preexisting isospin order only weakly, leaving the basic phase diagram intact while catalyzing the formation of topologically nontrivial gapped states whenever itinerant half- or quarter metal states occur at half- or quarter superlattice band filling. Our results show that rhombohedral trilayer graphene is an ideal platform for well-controlled tests of many-body theory and reveal magnetism in moiré materials to be fundamentally itinerant in nature."}],"type":"journal_article","oa_version":"Preprint","status":"public","title":"Half and quarter metals in rhombohedral trilayer graphene","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10025"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10076","title":"Reactive key-loss protection in blockchains","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase Commit()→Reveal()→Claim()−or−Challenge() smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP).","lang":"eng"}],"citation":{"ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: FC 2021 Workshops. Vol 12676. Springer Nature; 2021:431-450. doi:10.1007/978-3-662-63958-0_34","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In FC 2021 Workshops (Vol. 12676, pp. 431–450). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-63958-0_34","ieee":"S. Blackshear et al., “Reactive key-loss protection in blockchains,” in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450.","mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” FC 2021 Workshops, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:10.1007/978-3-662-63958-0_34.","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In FC 2021 Workshops, 12676:431–50. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-63958-0_34."},"publication":"FC 2021 Workshops","page":"431-450","date_published":"2021-09-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"17","year":"2021","acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Blackshear, Sam","last_name":"Blackshear","first_name":"Sam"},{"full_name":"Chalkias, Konstantinos","last_name":"Chalkias","first_name":"Konstantinos"},{"full_name":"Chatzigiannis, Panagiotis","last_name":"Chatzigiannis","first_name":"Panagiotis"},{"last_name":"Faizullabhoy","first_name":"Riyaz","full_name":"Faizullabhoy, Riyaz"},{"first_name":"Irakliy","last_name":"Khaburzaniya","full_name":"Khaburzaniya, Irakliy"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Lind, Joshua","last_name":"Lind","first_name":"Joshua"},{"last_name":"Wong","first_name":"David","full_name":"Wong, David"},{"first_name":"Tim","last_name":"Zakian","full_name":"Zakian, Tim"}],"volume":"12676 ","date_created":"2021-10-03T22:01:24Z","date_updated":"2023-08-14T07:06:16Z","main_file_link":[{"open_access":"1","url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/"}],"external_id":{"isi":["000713005000034"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-662-63958-0_34","conference":{"name":"FC: International Conference on Financial Cryptography and Data Security","location":"Virtual","start_date":"2021-03-01","end_date":"2021-03-05"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-6626-3957-3"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-662-63958-0"]},"month":"09"},{"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000703896600005"],"arxiv":["2008.01492"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01492","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2021.109234","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"month":"09","publisher":"Elsevier","department":[{"_id":"JaMa"}],"publication_status":"published","acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","year":"2021","volume":281,"date_updated":"2023-08-14T07:05:44Z","date_created":"2021-10-03T22:01:21Z","author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo"},{"last_name":"Suzuki","first_name":"Kohei","full_name":"Suzuki, Kohei"}],"article_number":"109234","ec_funded":1,"article_type":"original","citation":{"chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109234.","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” Journal of Functional Analysis, vol. 281, no. 11, 109234, Elsevier, 2021, doi:10.1016/j.jfa.2021.109234.","short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234.","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” Journal of Functional Analysis, vol. 281, no. 11. Elsevier, 2021.","apa":"Dello Schiavo, L., & Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109234","ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 2021;281(11). doi:10.1016/j.jfa.2021.109234"},"publication":"Journal of Functional Analysis","date_published":"2021-09-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","intvolume":" 281","status":"public","title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","_id":"10070","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms."}]},{"article_number":"2106858","file_date_updated":"2022-02-03T13:16:14Z","ec_funded":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"year":"2021","acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","pmid":1,"date_updated":"2023-08-14T07:25:27Z","date_created":"2021-10-11T20:07:24Z","volume":33,"author":[{"first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu"},{"full_name":"Calcabrini, Mariano","first_name":"Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877"},{"full_name":"Yu, Yuan","first_name":"Yuan","last_name":"Yu"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Cojocaru‐Mirédin, Oana","last_name":"Cojocaru‐Mirédin","first_name":"Oana"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"}],"related_material":{"record":[{"id":"12885","relation":"dissertation_contains","status":"public"}]},"month":"12","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"external_id":{"isi":["000709899300001"],"pmid":["34626034"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1002/adma.202106858","type":"journal_article","abstract":[{"text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials.","lang":"eng"}],"issue":"52","status":"public","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"intvolume":" 33","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10123","file":[{"file_id":"10720","relation":"main_file","date_updated":"2022-02-03T13:16:14Z","date_created":"2022-02-03T13:16:14Z","success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","file_name":"2021_AdvancedMaterials_Liu.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":5595666}],"oa_version":"Published Version","keyword":["mechanical engineering","mechanics of materials","general materials science"],"scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","publication":"Advanced Materials","citation":{"chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials. Wiley, 2021. https://doi.org/10.1002/adma.202106858.","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” Advanced Materials, vol. 33, no. 52, 2106858, Wiley, 2021, doi:10.1002/adma.202106858.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106858","ieee":"Y. Liu et al., “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” Advanced Materials, vol. 33, no. 52. Wiley, 2021.","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 2021;33(52). doi:10.1002/adma.202106858"},"date_published":"2021-12-29T00:00:00Z"},{"doi":"10.1016/J.JBC.2021.101094","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000706409200006"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"month":"09","author":[{"full_name":"Artan, Murat","first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992"},{"id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen","last_name":"Barratt","full_name":"Barratt, Stephen"},{"full_name":"Flynn, Sean M.","last_name":"Flynn","first_name":"Sean M."},{"last_name":"Begum","first_name":"Farida","full_name":"Begum, Farida"},{"last_name":"Skehel","first_name":"Mark","full_name":"Skehel, Mark"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas"},{"first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario"}],"volume":297,"date_created":"2021-10-10T22:01:23Z","date_updated":"2023-08-14T07:24:09Z","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","year":"2021","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"file_date_updated":"2021-10-11T12:20:58Z","article_number":"101094","date_published":"2021-09-01T00:00:00Z","citation":{"mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry, vol. 297, no. 3, 101094, Elsevier, 2021, doi:10.1016/J.JBC.2021.101094.","short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” Journal of Biological Chemistry. Elsevier, 2021. https://doi.org/10.1016/J.JBC.2021.101094.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 2021;297(3). doi:10.1016/J.JBC.2021.101094","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ieee":"M. Artan et al., “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” Journal of Biological Chemistry, vol. 297, no. 3. Elsevier, 2021.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., & de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. Elsevier. https://doi.org/10.1016/J.JBC.2021.101094"},"publication":"Journal of Biological Chemistry","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"10121","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","success":1,"date_created":"2021-10-11T12:20:58Z","date_updated":"2021-10-11T12:20:58Z","access_level":"open_access","file_name":"2021_JBC_Artan.pdf","content_type":"application/pdf","file_size":1680010,"creator":"cchlebak"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10117","intvolume":" 297","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","ddc":["612"],"status":"public","issue":"3","abstract":[{"lang":"eng","text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism."}],"type":"journal_article"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"_id":"10108","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Differential monitoring","ddc":["005"],"status":"public","intvolume":" 12974","oa_version":"Preprint","file":[{"file_name":"differentialmonitoring-cameraready-openaccess.pdf","access_level":"open_access","creator":"fmuehlbo","file_size":350632,"content_type":"application/pdf","file_id":"10109","relation":"main_file","date_updated":"2021-10-07T23:32:18Z","date_created":"2021-10-07T23:32:18Z","success":1,"checksum":"554c7fdb259eda703a8b6328a6dad55a"}],"scopus_import":"1","keyword":["run-time verification","software engineering","implicit specification"],"day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"International Conference on Runtime Verification","citation":{"ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_12","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In International Conference on Runtime Verification, 12974:231–43. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:10.1007/978-3-030-88494-9_12."},"page":"231-243","date_published":"2021-10-06T00:00:00Z","place":"Cham","file_date_updated":"2021-10-07T23:32:18Z","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","year":"2021","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","author":[{"last_name":"Mühlböck","first_name":"Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","full_name":"Mühlböck, Fabian"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"related_material":{"record":[{"status":"public","relation":"extended_version","id":"9946"}]},"date_updated":"2023-08-14T07:20:30Z","date_created":"2021-10-07T23:30:10Z","volume":12974,"month":"10","publication_identifier":{"isbn":["978-3-030-88493-2"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-88494-9"]},"oa":1,"external_id":{"isi":["000719383800012"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2021-10-11","location":"Virtual","end_date":"2021-10-14","name":"RV: Runtime Verification"},"doi":"10.1007/978-3-030-88494-9_12","language":[{"iso":"eng"}]},{"article_number":"e68238","ec_funded":1,"file_date_updated":"2021-10-11T14:15:07Z","pmid":1,"year":"2021","acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Vuong-Brender, Thanh","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","last_name":"Vuong-Brender","first_name":"Thanh"},{"last_name":"Flynn","first_name":"Sean","full_name":"Flynn, Sean"},{"first_name":"Yvonne","last_name":"Vallis","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","full_name":"Vallis, Yvonne"},{"full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","first_name":"Mario"}],"volume":10,"date_updated":"2023-08-14T07:23:39Z","date_created":"2021-10-10T22:01:22Z","publication_identifier":{"eissn":["2050-084X"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.7554/eLife.68238","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10116","intvolume":" 10","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","status":"public","ddc":["610"],"file":[{"date_updated":"2021-10-11T14:15:07Z","date_created":"2021-10-11T14:15:07Z","checksum":"b465e172d2b1f57aa26a2571a085d052","success":1,"relation":"main_file","file_id":"10122","file_size":1774624,"content_type":"application/pdf","creator":"cchlebak","file_name":"2021_eLife_VuongBrender.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"17","citation":{"ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 2021;10. doi:10.7554/eLife.68238","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., & de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.68238","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife, vol. 10, e68238, eLife Sciences Publications, 2021, doi:10.7554/eLife.68238.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.68238."},"publication":"eLife","article_type":"original","date_published":"2021-09-17T00:00:00Z"},{"article_type":"original","citation":{"chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses. MDPI, 2021. https://doi.org/10.3390/v13091853.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” Viruses, vol. 13, no. 9, 1853, MDPI, 2021, doi:10.3390/v13091853.","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” Viruses, vol. 13, no. 9. MDPI, 2021.","apa":"Obr, M., Schur, F. K., & Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. MDPI. https://doi.org/10.3390/v13091853","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 2021;13(9). doi:10.3390/v13091853"},"publication":"Viruses","date_published":"2021-09-17T00:00:00Z","keyword":["virology","infectious diseases"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"17","intvolume":" 13","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","status":"public","ddc":["616"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10103","oa_version":"Published Version","file":[{"date_updated":"2021-10-08T10:38:15Z","date_created":"2021-10-08T10:38:15Z","success":1,"checksum":"bcfd72a12977d48e22df3d0cc55aacf1","file_id":"10115","relation":"main_file","creator":"cchlebak","file_size":4146796,"content_type":"application/pdf","file_name":"2021_Viruses_Obr.pdf","access_level":"open_access"}],"type":"journal_article","issue":"9","abstract":[{"text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000699841100001"],"pmid":["34578434"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/v13091853","publication_identifier":{"issn":["1999-4915"]},"month":"09","publisher":"MDPI","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","year":"2021","volume":13,"date_created":"2021-10-07T09:13:29Z","date_updated":"2023-08-14T07:21:51Z","author":[{"last_name":"Obr","first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."}],"article_number":"1853","file_date_updated":"2021-10-08T10:38:15Z"},{"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"09","external_id":{"arxiv":["2107.05735"],"isi":["000704414400002"]},"main_file_link":[{"url":"https://arxiv.org/abs/2107.05735","open_access":"1"}],"oa":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1103/physrevb.104.104205","language":[{"iso":"eng"}],"article_number":"104205","ec_funded":1,"acknowledgement":"We would like to thank S. De Nicola, P. Brighi, and V. Karle for fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges support from the US Department of Energy, Office of Science, Basic Energy Sciences, under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through a Sloan Research Fellowship.","year":"2021","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A"},{"full_name":"Vasseur, Romain","last_name":"Vasseur","first_name":"Romain"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"volume":104,"date_created":"2021-10-02T09:03:42Z","date_updated":"2023-08-14T07:24:47Z","article_processing_charge":"No","day":"30","citation":{"ieee":"R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from restricted Boltzmann machines,” Physical Review B, vol. 104, no. 10. American Physical Society, 2021.","apa":"Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2021). Entanglement transitions from restricted Boltzmann machines. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.104205","ista":"Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 104205.","ama":"Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 2021;104(10). doi:10.1103/physrevb.104.104205","chicago":"Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.104205.","short":"R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).","mla":"Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann Machines.” Physical Review B, vol. 104, no. 10, 104205, American Physical Society, 2021, doi:10.1103/physrevb.104.104205."},"publication":"Physical Review B","article_type":"original","date_published":"2021-09-30T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"The search for novel entangled phases of matter has lead to the recent discovery of a new class of “entanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r^α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10067","intvolume":" 104","status":"public","title":"Entanglement transitions from restricted Boltzmann machines","oa_version":"Preprint"},{"publication_identifier":{"issn":["2664-1690"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9946","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"oa":1,"file_date_updated":"2021-09-03T12:34:28Z","date_created":"2021-08-20T20:00:37Z","date_updated":"2023-08-14T07:20:29Z","related_material":{"record":[{"status":"public","relation":"other","id":"9281"},{"relation":"shorter_version","status":"public","id":"10108"}]},"author":[{"full_name":"Mühlböck, Fabian","first_name":"Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"publisher":"IST Austria","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","year":"2021","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["run-time verification","software engineering","implicit specification"],"date_published":"2021-09-01T00:00:00Z","page":"17","citation":{"ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946."},"abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file":[{"creator":"fmuehlbo","file_size":"320453","content_type":"application/pdf","access_level":"open_access","file_name":"differentialmonitoring-techreport.pdf","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_created":"2021-08-20T19:59:44Z","date_updated":"2021-09-03T12:34:28Z","file_id":"9948","relation":"main_file"}],"oa_version":"Published Version","title":"Differential monitoring","ddc":["005"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9946"},{"abstract":[{"lang":"eng","text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics."}],"issue":"18","type":"journal_article","oa_version":"Published Version","file":[{"file_size":4404141,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_Materials_Chang.pdf","checksum":"4929dfc673a3ae77c010b6174279cc1d","success":1,"date_updated":"2021-10-14T11:56:39Z","date_created":"2021-10-14T11:56:39Z","relation":"main_file","file_id":"10140"}],"_id":"10073","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["540"],"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","intvolume":" 14","day":"19","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-09-19T00:00:00Z","publication":"Materials","citation":{"ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021.","apa":"Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416","chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416.","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416.","short":"C. Chang, M. Ibáñez, Materials 14 (2021)."},"article_type":"original","file_date_updated":"2021-10-14T11:56:39Z","article_number":"5416","author":[{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","first_name":"Cheng"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-10-03T22:01:23Z","date_updated":"2023-08-14T08:00:01Z","volume":14,"acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","year":"2021","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"MaIb"}],"month":"09","publication_identifier":{"eissn":["1996-1944"]},"doi":"10.3390/ma14185416","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34576640"],"isi":["000700689400001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}]},{"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","status":"public","ddc":["610"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10167","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1008594,"content_type":"application/pdf","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","access_level":"open_access","date_created":"2022-05-06T09:47:18Z","date_updated":"2022-05-06T09:47:18Z","success":1,"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_id":"11352","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"article_type":"original","publication":"Molecular Biology and Evolution","citation":{"chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press . https://doi.org/10.1093/molbev/msab178","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” Molecular Biology and Evolution. Oxford University Press , 2021.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178"},"date_published":"2021-06-19T00:00:00Z","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Oxford University Press ","department":[{"_id":"BeVi"}],"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","year":"2021","pmid":1,"date_created":"2021-10-21T07:49:12Z","date_updated":"2023-08-14T08:03:06Z","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"last_name":"Moldovan","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"file_date_updated":"2022-05-06T09:47:18Z","quality_controlled":"1","isi":1,"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msab178","month":"06","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]}},{"day":"19","article_processing_charge":"No","has_accepted_license":"1","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"date_published":"2021-10-19T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2","ieee":"L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021)."},"abstract":[{"text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2021-10-21T13:51:49Z","date_updated":"2021-10-21T13:51:49Z","checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"relation":"main_file","file_id":"10169","content_type":"application/pdf","file_size":5111706,"creator":"cchlebak","file_name":"2021_NatComm_Appel.pdf","access_level":"open_access"}],"ddc":["610"],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","status":"public","intvolume":" 12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10163","month":"10","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26360-2","isi":1,"quality_controlled":"1","external_id":{"isi":["000709050300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-10-21T13:51:49Z","article_number":"6078","date_updated":"2023-08-14T08:02:31Z","date_created":"2021-10-20T14:40:32Z","volume":12,"author":[{"full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie","last_name":"Appel"},{"full_name":"Franke, Vedran","last_name":"Franke","first_name":"Vedran"},{"last_name":"Bruno","first_name":"Melania","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Kasiliauskaite, Aiste","last_name":"Kasiliauskaite","first_name":"Aiste"},{"full_name":"Kaufmann, Tanja","last_name":"Kaufmann","first_name":"Tanja"},{"first_name":"Ursula E.","last_name":"Schoeberl","full_name":"Schoeberl, Ursula E."},{"full_name":"Puchinger, Martin G.","last_name":"Puchinger","first_name":"Martin G."},{"full_name":"Kostrhon, Sebastian","first_name":"Sebastian","last_name":"Kostrhon"},{"full_name":"Ebenwaldner, Carmen","first_name":"Carmen","last_name":"Ebenwaldner"},{"full_name":"Sebesta, Marek","first_name":"Marek","last_name":"Sebesta"},{"full_name":"Beltzung, Etienne","first_name":"Etienne","last_name":"Beltzung"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"full_name":"Lin, Gen","last_name":"Lin","first_name":"Gen"},{"first_name":"Anna","last_name":"Vlasova","full_name":"Vlasova, Anna"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"},{"full_name":"Pavri, Rushad","first_name":"Rushad","last_name":"Pavri"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"full_name":"Akalin, Altuna","last_name":"Akalin","first_name":"Altuna"},{"last_name":"Stefl","first_name":"Richard","full_name":"Stefl, Richard"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"first_name":"Dea","last_name":"Slade","full_name":"Slade, Dea"}],"related_material":{"link":[{"relation":"earlier_version","description":"Preprint ","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159"}]},"publication_status":"published","department":[{"_id":"CaBe"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S."},{"article_type":"original","page":"205-219","publication":"Computer Graphics Forum","citation":{"ama":"Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626","ista":"Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219.","ieee":"T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021.","apa":"Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626","mla":"Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626.","short":"T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219.","chicago":"Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626."},"date_published":"2021-05-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","title":"Neural acceleration of scattering-aware color 3D printing","ddc":["004"],"status":"public","intvolume":" 40","_id":"9547","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","access_level":"open_access","content_type":"application/pdf","file_size":26026501,"creator":"bbickel","relation":"main_file","file_id":"10120","date_created":"2021-10-11T12:06:50Z","date_updated":"2021-10-11T12:06:50Z","checksum":"33271724215f54a75c39d2ed40f2c502","success":1}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time.","lang":"eng"}],"issue":"2","isi":1,"quality_controlled":"1","project":[{"grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"external_id":{"isi":["000657959600017"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.142626","month":"05","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Wiley","year":"2021","acknowledgement":"We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","date_updated":"2023-08-14T08:01:50Z","date_created":"2021-06-13T22:01:32Z","volume":40,"author":[{"full_name":"Rittig, Tobias","first_name":"Tobias","last_name":"Rittig"},{"full_name":"Sumin, Denis","first_name":"Denis","last_name":"Sumin"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"last_name":"Voloboy","first_name":"Alexey","full_name":"Voloboy, Alexey"},{"last_name":"Wilkie","first_name":"Alexander","full_name":"Wilkie, Alexander"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"file_date_updated":"2021-10-11T12:06:50Z","ec_funded":1},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"isi":1,"quality_controlled":"1","doi":"10.1126/sciadv.abj0127","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["23752548"]},"year":"2021","acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"American Association for the Advancement of Science","author":[{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"last_name":"Álvarez-Pérez","first_name":"Gonzalo","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"full_name":"Ma, Weiliang","first_name":"Weiliang","last_name":"Ma"},{"first_name":"Qiaoliang","last_name":"Bao","full_name":"Bao, Qiaoliang"},{"full_name":"Volkov, Valentyn S.","last_name":"Volkov","first_name":"Valentyn S."},{"full_name":"Hillenbrand, Rainer","first_name":"Rainer","last_name":"Hillenbrand"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"date_created":"2021-10-24T22:01:33Z","date_updated":"2023-08-14T08:04:42Z","volume":7,"article_number":"abj0127","file_date_updated":"2021-10-27T14:16:06Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Science Advances","citation":{"chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127.","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127.","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","ieee":"J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127"},"article_type":"original","date_published":"2021-10-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"Yes","has_accepted_license":"1","_id":"10177","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["530"],"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","intvolume":" 7","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2441163,"creator":"cziletti","access_level":"open_access","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"date_created":"2021-10-27T14:16:06Z","date_updated":"2021-10-27T14:16:06Z","relation":"main_file","file_id":"10189"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials."}],"issue":"41"},{"ec_funded":1,"volume":598,"date_created":"2021-10-17T22:01:17Z","date_updated":"2023-08-14T08:01:21Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","relation":"press_release","description":"News on IST Webpage"}]},"author":[{"first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"department":[{"_id":"LeSa"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","year":"2021","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"10","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"doi":"10.1038/s41586-021-03927-z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"issue":"7880","abstract":[{"lang":"eng","text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain."}],"type":"journal_article","oa_version":"None","intvolume":" 598","status":"public","title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","_id":"10146","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2021-10-14T00:00:00Z","page":"364-367","article_type":"original","citation":{"chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","apa":"Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z"},"publication":"Nature"},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Journal of Mathematical Physics","citation":{"ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP Publishing, 2021.","apa":"Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0037826","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826.","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826."},"date_published":"2021-10-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact."}],"issue":"10","status":"public","title":"Topological field theory on r-spin surfaces and the Arf-invariant","intvolume":" 62","_id":"10176","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"10","publication_identifier":{"issn":["00222488"]},"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1063/5.0037826","article_number":"102302","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","year":"2021","date_created":"2021-10-24T22:01:32Z","date_updated":"2023-08-14T08:04:12Z","volume":62,"author":[{"first_name":"Ingo","last_name":"Runkel","full_name":"Runkel, Ingo"},{"orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","last_name":"Szegedy","first_name":"Lorant","full_name":"Szegedy, Lorant"}]},{"year":"2021","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","pmid":1,"publication_status":"published","publisher":"Embo Press","department":[{"_id":"Bio"}],"author":[{"first_name":"Sunanjay","last_name":"Bajaj","full_name":"Bajaj, Sunanjay"},{"full_name":"Bagley, Joshua A.","last_name":"Bagley","first_name":"Joshua A."},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vertesy","first_name":"Abel","full_name":"Vertesy, Abel"},{"full_name":"Nagumo Wong, Sakurako","last_name":"Nagumo Wong","first_name":"Sakurako"},{"last_name":"Krenn","first_name":"Veronica","full_name":"Krenn, Veronica"},{"last_name":"Lévi-Strauss","first_name":"Julie","full_name":"Lévi-Strauss, Julie"},{"full_name":"Knoblich, Juergen A.","first_name":"Juergen A.","last_name":"Knoblich"}],"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:05:23Z","volume":40,"article_number":"e108714","file_date_updated":"2021-12-13T14:54:14Z","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.15252/embj.2021108714","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10179","ddc":["610"],"status":"public","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","intvolume":" 40","file":[{"creator":"alisjak","file_size":7819881,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_EMBO_Bajaj.pdf","success":1,"checksum":"78d2d02e775322297e774f72810a41a4","date_created":"2021-12-13T14:54:14Z","date_updated":"2021-12-13T14:54:14Z","file_id":"10541","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling.","lang":"eng"}],"issue":"23","publication":"EMBO Journal","citation":{"chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714.","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714.","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714"},"article_type":"original","date_published":"2021-10-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1"},{"_id":"10203","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","ddc":["530"],"status":"public","intvolume":" 12","file":[{"creator":"cchlebak","file_size":1434201,"content_type":"application/pdf","file_name":"2021_NatComm_Sortino.pdf","access_level":"open_access","date_created":"2021-11-03T11:31:24Z","date_updated":"2021-11-03T11:31:24Z","success":1,"checksum":"8580d128389860f732028c521cd5949e","file_id":"10212","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors.","lang":"eng"}],"publication":"Nature Communications","citation":{"ama":"Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3","ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063.","apa":"Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3","ieee":"L. Sortino et al., “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” Nature Communications, vol. 12. Springer Nature, 2021.","mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3.","short":"L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021).","chicago":"Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3."},"article_type":"original","date_published":"2021-10-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"author":[{"last_name":"Sortino","first_name":"Luca","full_name":"Sortino, Luca"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"last_name":"Phillips","first_name":"Catherine L.","full_name":"Phillips, Catherine L."},{"full_name":"Brash, Alistair J.","first_name":"Alistair J.","last_name":"Brash"},{"full_name":"Cambiasso, Javier","first_name":"Javier","last_name":"Cambiasso"},{"first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","orcid":"0000-0001-7173-4923","full_name":"Marensi, Elena"},{"last_name":"Fox","first_name":"A. Mark","full_name":"Fox, A. Mark"},{"last_name":"Maier","first_name":"Stefan A.","full_name":"Maier, Stefan A."},{"last_name":"Sapienza","first_name":"Riccardo","full_name":"Sapienza, Riccardo"},{"last_name":"Tartakovskii","first_name":"Alexander I.","full_name":"Tartakovskii, Alexander I."}],"date_created":"2021-10-31T23:01:30Z","date_updated":"2023-08-14T08:12:12Z","volume":12,"article_number":"6063","file_date_updated":"2021-11-03T11:31:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000708601800015"],"arxiv":["2103.16986"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-021-26262-3","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2041-1723"]}},{"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"29","article_type":"original","citation":{"ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021.","apa":"Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1."},"publication":"New Journal of Physics","date_published":"2021-09-29T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.","lang":"eng"}],"intvolume":" 23","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10178","oa_version":"Published Version","file":[{"file_id":"10193","relation":"main_file","date_updated":"2021-10-28T12:06:01Z","date_created":"2021-10-28T12:06:01Z","success":1,"checksum":"ace603e8f0962b3ba55f23fa34f57764","file_name":"2021_NewJPhys_Sahu.pdf","access_level":"open_access","creator":"cziletti","file_size":2215016,"content_type":"application/pdf"}],"publication_identifier":{"eissn":["13672630"]},"month":"09","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"language":[{"iso":"eng"}],"doi":"10.1088/1367-2630/ac23f1","article_number":"093043","file_date_updated":"2021-10-28T12:06:01Z","publisher":"IOP Publishing","department":[{"_id":"EdHa"}],"publication_status":"published","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","year":"2021","volume":23,"date_created":"2021-10-24T22:01:34Z","date_updated":"2023-08-14T08:10:31Z","author":[{"full_name":"Sahu, Preeti","first_name":"Preeti","last_name":"Sahu","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"last_name":"Schwarz","first_name":"J. M.","full_name":"Schwarz, J. M."},{"full_name":"Manning, M. Lisa","last_name":"Manning","first_name":"M. Lisa"}]},{"status":"public","title":"Rectifiable curves in proximally smooth sets","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10181","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space."}],"article_type":"original","publication":"Set-Valued and Variational Analysis","citation":{"ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021.","apa":"Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1","ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021. https://doi.org/10.1007/s11228-021-00612-1.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021, doi:10.1007/s11228-021-00612-1."},"date_published":"2021-10-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","year":"2021","date_updated":"2023-08-14T08:11:38Z","date_created":"2021-10-24T22:01:35Z","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"first_name":"Mariana S.","last_name":"Lopushanski","full_name":"Lopushanski, Mariana S."}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2012.10691"],"isi":["000705774800001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10691"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11228-021-00612-1","month":"10","publication_identifier":{"issn":["0927-6947"],"eissn":["1877-0541"]}},{"intvolume":" 12","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10202","file":[{"date_created":"2021-11-09T13:59:26Z","date_updated":"2021-11-09T13:59:26Z","success":1,"checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_id":"10262","relation":"main_file","creator":"cziletti","file_size":7144437,"content_type":"application/pdf","file_name":"2021_NatureComm_Pradhan.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.","lang":"eng"}],"article_type":"original","citation":{"ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","ieee":"S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7.","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7.","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021)."},"publication":"Nature Communications","date_published":"2021-10-19T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"19","publisher":"Springer Nature","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","volume":12,"date_created":"2021-10-31T23:01:29Z","date_updated":"2023-08-14T10:32:48Z","related_material":{"link":[{"description":"Preprint","relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 "}]},"author":[{"full_name":"Pradhan, Saurabh J.","last_name":"Pradhan","first_name":"Saurabh J."},{"first_name":"Puli Chandramouli","last_name":"Reddy","full_name":"Reddy, Puli Chandramouli"},{"full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael","orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sharma, Ankita","last_name":"Sharma","first_name":"Ankita"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","first_name":"Keisuke","last_name":"Sako","full_name":"Sako, Keisuke"},{"full_name":"Oak, Meghana S.","last_name":"Oak","first_name":"Meghana S."},{"full_name":"Shah, Rini","last_name":"Shah","first_name":"Rini"},{"first_name":"Mrinmoy","last_name":"Pal","full_name":"Pal, Mrinmoy"},{"last_name":"Deshpande","first_name":"Ojas","full_name":"Deshpande, Ojas"},{"full_name":"Dsilva, Greg","first_name":"Greg","last_name":"Dsilva"},{"first_name":"Yin","last_name":"Tang","full_name":"Tang, Yin"},{"full_name":"Mishra, Rakesh","first_name":"Rakesh","last_name":"Mishra"},{"full_name":"Deshpande, Girish","first_name":"Girish","last_name":"Deshpande"},{"full_name":"Giraldez, Antonio J.","last_name":"Giraldez","first_name":"Antonio J."},{"first_name":"Mahendra","last_name":"Sonawane","full_name":"Sonawane, Mahendra"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Galande, Sanjeev","last_name":"Galande","first_name":"Sanjeev"}],"article_number":"6094","file_date_updated":"2021-11-09T13:59:26Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000709050300016"],"pmid":["34667153"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26234-7","publication_identifier":{"eissn":["20411723"]},"month":"10"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions."}],"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","status":"public","ddc":["610"],"intvolume":" 12","_id":"10271","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":2397203,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_FrontiersMicrob_Qi.pdf","checksum":"d41321748e9588dd3cf03e9a7222127f","success":1,"date_created":"2021-11-11T10:54:40Z","date_updated":"2021-11-11T10:54:40Z","relation":"main_file","file_id":"10272"}],"oa_version":"Published Version","keyword":["microbiology"],"scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Frontiers in Microbiology","citation":{"chicago":"Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017.","short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","mla":"Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology, vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017.","ieee":"Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021.","apa":"Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017","ista":"Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017.","ama":"Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017"},"date_published":"2021-10-20T00:00:00Z","article_number":"760017","file_date_updated":"2021-11-11T10:54:40Z","ec_funded":1,"publication_status":"published","publisher":"Frontiers","year":"2021","acknowledgement":"High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support.","pmid":1,"date_created":"2021-11-11T10:39:37Z","date_updated":"2023-08-14T11:43:23Z","volume":12,"author":[{"id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416","first_name":"Qin","last_name":"Qi","full_name":"Qi, Qin"},{"full_name":"Angermayr, S. Andreas","first_name":"S. Andreas","last_name":"Angermayr"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"month":"10","publication_identifier":{"eissn":["1664-302X"]},"isi":1,"quality_controlled":"1","project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000715997300001"],"pmid":["34745067"]},"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2021.760017"},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"29","citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z.","ama":"Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048. doi:10.1007/s00220-021-04239-z","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04239-z","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” Communications in Mathematical Physics, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048."},"publication":"Communications in Mathematical Physics","page":"1005–1048","article_type":"original","date_published":"2021-10-29T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"text":"We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).","lang":"eng"}],"_id":"10221","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 388","status":"public","ddc":["510"],"title":"Eigenstate thermalization hypothesis for Wigner matrices","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":841426,"access_level":"open_access","file_name":"2021_CommunMathPhys_Cipolloni.pdf","success":1,"checksum":"a2c7b6f5d23b5453cd70d1261272283b","date_updated":"2022-02-02T10:19:55Z","date_created":"2022-02-02T10:19:55Z","file_id":"10715","relation":"main_file"}],"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000712232700001"],"arxiv":["2012.13215"]},"oa":1,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00220-021-04239-z","language":[{"iso":"eng"}],"file_date_updated":"2022-02-02T10:19:55Z","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"volume":388,"date_updated":"2023-08-14T10:29:49Z","date_created":"2021-11-07T23:01:25Z"},{"intvolume":" 242","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","ddc":["530"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10224","oa_version":"Published Version","file":[{"creator":"alisjak","file_size":990529,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Springer_Feliciangeli.pdf","success":1,"checksum":"672e9c21b20f1a50854b7c821edbb92f","date_created":"2021-12-14T08:35:42Z","date_updated":"2021-12-14T08:35:42Z","file_id":"10544","relation":"main_file"}],"type":"journal_article","issue":"3","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"page":"1835–1906","article_type":"original","citation":{"chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:10.1007/s00205-021-01715-7.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.","apa":"Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7"},"publication":"Archive for Rational Mechanics and Analysis","date_published":"2021-10-25T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"25","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","volume":242,"date_updated":"2023-08-14T10:32:19Z","date_created":"2021-11-07T23:01:26Z","related_material":{"record":[{"id":"9787","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"ec_funded":1,"file_date_updated":"2021-12-14T08:35:42Z","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2101.12566"],"isi":["000710850600001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00205-021-01715-7","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"month":"10"},{"abstract":[{"lang":"eng","text":"Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems"}],"issue":"11","type":"journal_article","alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"file":[{"access_level":"open_access","file_name":"2021_Genes_Vasic.pdf","creator":"dernst","file_size":1335308,"content_type":"application/pdf","file_id":"11380","relation":"main_file","success":1,"checksum":"256cb832a9c3051c7dc741f6423b8cbd","date_created":"2022-05-16T07:02:27Z","date_updated":"2022-05-16T07:02:27Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10281","ddc":["570"],"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","status":"public","intvolume":" 12","day":"30","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-10-30T00:00:00Z","publication":"Genes","citation":{"ama":"Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 2021;12(11). doi:10.3390/genes12111746","apa":"Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. MDPI. https://doi.org/10.3390/genes12111746","ieee":"V. Vasic et al., “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” Genes, vol. 12, no. 11. MDPI, 2021.","ista":"Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","mla":"Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes, vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.","chicago":"Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746."},"article_type":"original","file_date_updated":"2022-05-16T07:02:27Z","ec_funded":1,"article_number":"1746","author":[{"last_name":"Vasic","first_name":"Verica","full_name":"Vasic, Verica"},{"last_name":"Jones","first_name":"Mattson S.O.","full_name":"Jones, Mattson S.O."},{"full_name":"Haslinger, Denise","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","first_name":"Denise","last_name":"Haslinger"},{"full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus"},{"full_name":"Schmeisser, Michael J.","last_name":"Schmeisser","first_name":"Michael J."},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"first_name":"Andreas G.","last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G."}],"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:46:12Z","volume":12,"year":"2021","acknowledgement":"This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.","publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"MDPI","month":"10","publication_identifier":{"eissn":["2073-4425"]},"doi":"10.3390/genes12111746","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000834044200002"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}]},{"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:46:43Z","volume":233,"author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan"},{"last_name":"Retzer","first_name":"Katarzyna","full_name":"Retzer, Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"first_name":"Aswathy","last_name":"Jayasree","full_name":"Jayasree, Aswathy"},{"full_name":"Filepová, Roberta","last_name":"Filepová","first_name":"Roberta"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"},{"full_name":"Rombaut, Debbie","last_name":"Rombaut","first_name":"Debbie"},{"full_name":"Jacobs, Thomas B.","first_name":"Thomas B.","last_name":"Jacobs"},{"last_name":"Frilander","first_name":"Mikko J.","full_name":"Frilander, Mikko J."},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Kamil","last_name":"Růžička","full_name":"Růžička, Kamil"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","year":"2021","pmid":1,"month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.17792","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"abstract":[{"text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","status":"public","intvolume":" 233","_id":"10282","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"05","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-05T00:00:00Z","article_type":"original","page":"329-343","publication":"New Phytologist","citation":{"apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021.","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792."}},{"publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions.","year":"2021","volume":245,"date_created":"2021-11-07T23:01:24Z","date_updated":"2023-08-14T11:43:55Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8183"},{"status":"public","relation":"earlier_version","id":"9308"}]},"author":[{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"first_name":"Arkadiy B.","last_name":"Skopenkov","full_name":"Skopenkov, Arkadiy B."},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"project":[{"name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000712942100013"],"arxiv":["1511.03501"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"language":[{"iso":"eng"}],"doi":"10.1007/s11856-021-2216-z","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"month":"10","intvolume":" 245","status":"public","title":"Eliminating higher-multiplicity intersections. III. Codimension 2","_id":"10220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}],"page":"501–534 ","article_type":"original","citation":{"short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z.","chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z.","ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534."},"publication":"Israel Journal of Mathematics","date_published":"2021-10-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"30"},{"article_processing_charge":"No","day":"29","month":"10","date_published":"2021-10-29T00:00:00Z","doi":"10.5061/DRYAD.7PVMCVDTJ","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.7pvmcvdtj","open_access":"1"}],"citation":{"ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ","chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","mla":"Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ."},"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","related_material":{"record":[{"id":"10284","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez"},{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"},{"full_name":"Naiser, Filip","first_name":"Filip","last_name":"Naiser"},{"first_name":"Elisabeth","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth"},{"full_name":"Matas, Jiri","last_name":"Matas","first_name":"Jiri"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"oa_version":"Published Version","date_created":"2023-05-23T16:14:35Z","date_updated":"2023-08-14T11:45:28Z","_id":"13061","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SyCr"}],"publisher":"Dryad","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","ddc":["570"],"status":"public"},{"author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"full_name":"Dey, Partha N","last_name":"Dey","first_name":"Partha N"},{"last_name":"Elía-Zudaire","first_name":"Óscar","full_name":"Elía-Zudaire, Óscar"},{"full_name":"Garcia Rabaneda, Luis E","first_name":"Luis E","last_name":"Garcia Rabaneda","id":"33D1B084-F248-11E8-B48F-1D18A9856A87"},{"full_name":"García-Lira, Carmen","first_name":"Carmen","last_name":"García-Lira"},{"first_name":"Teddy","last_name":"Grand","full_name":"Grand, Teddy"},{"first_name":"Victor","last_name":"Briz","full_name":"Briz, Victor"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"full_name":"Andero Galí, Raül","last_name":"Andero Galí","first_name":"Raül"},{"first_name":"Sergio","last_name":"Niñerola","full_name":"Niñerola, Sergio"},{"last_name":"Barco","first_name":"Angel","full_name":"Barco, Angel"},{"full_name":"Paoletti, Pierre","first_name":"Pierre","last_name":"Paoletti"},{"first_name":"John F","last_name":"Wesseling","full_name":"Wesseling, John F"},{"first_name":"Fabrizio","last_name":"Gardoni","full_name":"Gardoni, Fabrizio"},{"first_name":"Steven J","last_name":"Tavalin","full_name":"Tavalin, Steven J"},{"first_name":"Isabel","last_name":"Perez-Otaño","full_name":"Perez-Otaño, Isabel"}],"volume":10,"date_created":"2021-11-18T06:59:45Z","date_updated":"2023-08-14T11:50:50Z","year":"2021","acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","department":[{"_id":"GaNo"}],"publisher":"eLife Sciences Publications","publication_status":"published","file_date_updated":"2021-11-18T07:02:02Z","article_number":"e71575","doi":"10.7554/elife.71575","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000720945900001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2050-084X"]},"month":"11","file":[{"creator":"lgarciar","content_type":"application/pdf","file_size":2477302,"file_name":"elife-71575-v1.pdf","access_level":"open_access","date_created":"2021-11-18T07:02:02Z","date_updated":"2021-11-18T07:02:02Z","success":1,"checksum":"59318e9e41507cec83c2f4070e6ad540","file_id":"10302","relation":"main_file"}],"oa_version":"Published Version","_id":"10301","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","ddc":["570"],"status":"public","abstract":[{"text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-17T00:00:00Z","citation":{"chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575.","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575.","ieee":"M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575"},"publication":"eLife","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"17","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"]},{"publication":"EMBO Reports","citation":{"ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824","chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021)."},"article_type":"original","date_published":"2021-11-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10283","ddc":["570"],"status":"public","title":"Towards best practices in research: Role of academic core facilities","intvolume":" 22","file":[{"date_created":"2022-05-16T07:07:41Z","date_updated":"2022-05-16T07:07:41Z","success":1,"checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381","relation":"main_file","creator":"dernst","file_size":488583,"content_type":"application/pdf","file_name":"2021_EmboReports_Restivo.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research."}],"external_id":{"isi":["000714350000001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.15252/embr.202153824","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"year":"2021","acknowledgement":"This EQIPD 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 program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","publication_status":"published","department":[{"_id":"PreCl"}],"publisher":"EMBO Press","author":[{"full_name":"Restivo, Leonardo","last_name":"Restivo","first_name":"Leonardo"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"full_name":"Tsoory, Michael","last_name":"Tsoory","first_name":"Michael"},{"full_name":"Bikovski, Lior","first_name":"Lior","last_name":"Bikovski"},{"last_name":"Badurek","first_name":"Sylvia","full_name":"Badurek, Sylvia"},{"full_name":"Pitzer, Claudia","last_name":"Pitzer","first_name":"Claudia"},{"full_name":"Kos-Braun, Isabelle C.","first_name":"Isabelle C.","last_name":"Kos-Braun"},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"full_name":"Ward, Jonathan","first_name":"Jonathan","last_name":"Ward"},{"first_name":"Michael","last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael"},{"last_name":"Noldus","first_name":"Lucas P.J.J.","full_name":"Noldus, Lucas P.J.J."},{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"last_name":"Voikar","first_name":"Vootele","full_name":"Voikar, Vootele"}],"date_created":"2021-11-14T23:01:24Z","date_updated":"2023-08-14T11:47:35Z","volume":22,"article_number":"e53824","file_date_updated":"2022-05-16T07:07:41Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"publication_identifier":{"issn":["2399-3642"]},"month":"03","doi":"10.1038/s42003-021-01808-9","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2021-11-19T15:09:18Z","article_number":"304","author":[{"full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"first_name":"Anna","last_name":"Frank","full_name":"Frank, Anna"},{"last_name":"Tanaka","first_name":"Hideaki","full_name":"Tanaka, Hideaki"},{"last_name":"Kawamoto","first_name":"Akihiro","full_name":"Kawamoto, Akihiro"},{"first_name":"Eithar","last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar"},{"last_name":"Kato","first_name":"Takayuki","full_name":"Kato, Takayuki"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Gerle, Christoph","first_name":"Christoph","last_name":"Gerle"},{"last_name":"Nowaczyk","first_name":"Marc M.","full_name":"Nowaczyk, Marc M."},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"}],"volume":4,"date_updated":"2023-08-14T11:51:19Z","date_created":"2021-11-19T11:37:29Z","pmid":1,"year":"2021","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","publisher":"Springer ","department":[{"_id":"LeSa"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"date_published":"2021-03-08T00:00:00Z","citation":{"apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9."},"publication":"Communications Biology","article_type":"original","issue":"1","abstract":[{"text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"10318","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"date_created":"2021-11-19T15:09:18Z","date_updated":"2021-11-19T15:09:18Z","access_level":"open_access","file_name":"2021_CommBio_Çoruh.pdf","file_size":6030261,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10310","intvolume":" 4","title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","ddc":["570"],"status":"public"},{"volume":10,"date_created":"2021-11-11T10:05:18Z","date_updated":"2023-08-14T11:49:23Z","author":[{"full_name":"Marconi, Marco","first_name":"Marco","last_name":"Marconi"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","first_name":"Marçal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"last_name":"Wabnik","first_name":"Krzysztof","full_name":"Wabnik, Krzysztof"}],"publisher":"eLife Sciences Publications","department":[{"_id":"EvBe"}],"publication_status":"published","pmid":1,"acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","year":"2021","file_date_updated":"2022-05-13T09:00:29Z","article_number":"72132","language":[{"iso":"eng"}],"doi":"10.7554/elife.72132","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34723798"],"isi":["000734671200001"]},"publication_identifier":{"issn":["2050-084X"]},"month":"11","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_eLife_Marconi.pdf","creator":"dernst","file_size":14137503,"content_type":"application/pdf","file_id":"11372","relation":"main_file","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_created":"2022-05-13T09:00:29Z","date_updated":"2022-05-13T09:00:29Z"}],"intvolume":" 10","ddc":["570"],"status":"public","title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","_id":"10270","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development."}],"type":"journal_article","date_published":"2021-11-01T00:00:00Z","article_type":"original","citation":{"mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132.","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132"},"publication":"eLife","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1"},{"keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"scopus_import":"1","day":"03","article_processing_charge":"No","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021.","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118."},"date_published":"2021-11-03T00:00:00Z","type":"journal_article","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"issue":"45","status":"public","title":"Experimental observation of the origin and structure of elastoinertial turbulence","intvolume":" 118","_id":"10299","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"11","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"}],"external_id":{"pmid":[" 34732570"],"isi":["000720926900019"],"arxiv":["2103.00023"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2102350118","article_number":"e2102350118","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","year":"2021","pmid":1,"date_updated":"2023-08-14T11:50:10Z","date_created":"2021-11-17T13:24:24Z","volume":118,"author":[{"full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul"},{"full_name":"Sankar, Sarath","first_name":"Sarath","last_name":"Sankar"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}]},{"abstract":[{"text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"date_updated":"2021-11-15T13:25:52Z","date_created":"2021-11-15T13:25:52Z","checksum":"1c392b12b9b7b615d422d9fabe19cdb9","success":1,"relation":"main_file","file_id":"10292","content_type":"application/pdf","file_size":6282703,"creator":"cchlebak","file_name":"2021_NatComm_Aubret.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["530"],"status":"public","title":"Metamachines of pluripotent colloids","intvolume":" 12","_id":"10280","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"04","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-11-04T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6.","apa":"Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6"},"file_date_updated":"2021-11-15T13:25:52Z","article_number":"6398","date_created":"2021-11-14T23:01:23Z","date_updated":"2023-08-14T11:48:37Z","volume":12,"author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"first_name":"Quentin","last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","orcid":"0000-0002-2916-6632","full_name":"Martinet, Quentin"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JePa"}],"acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","year":"2021","pmid":1,"month":"11","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26699-6","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"oa":1},{"pmid":1,"acknowledgement":"We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities.","year":"2021","publisher":"Public Library of Science","department":[{"_id":"MaDe"}],"publication_status":"published","related_material":{"record":[{"id":"13069","status":"public","relation":"research_data"}]},"author":[{"full_name":"Chauve, Laetitia","first_name":"Laetitia","last_name":"Chauve"},{"full_name":"Hodge, Francesca","last_name":"Hodge","first_name":"Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"last_name":"Masoudzadeh","first_name":"Fatemah","full_name":"Masoudzadeh, Fatemah"},{"first_name":"Harry Jack","last_name":"Mann","full_name":"Mann, Harry Jack"},{"full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo","first_name":"Andrea"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"full_name":"West, Greg","first_name":"Greg","last_name":"West"},{"last_name":"Sousa","first_name":"Bebiana C.","full_name":"Sousa, Bebiana C."},{"last_name":"Segonds-Pichon","first_name":"Anne","full_name":"Segonds-Pichon, Anne"},{"full_name":"Li, Cheryl","first_name":"Cheryl","last_name":"Li"},{"last_name":"Wingett","first_name":"Steven","full_name":"Wingett, Steven"},{"last_name":"Kienberger","first_name":"Hermine","full_name":"Kienberger, Hermine"},{"last_name":"Kleigrewe","first_name":"Karin","full_name":"Kleigrewe, Karin"},{"full_name":"De Bono, Mario","first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"},{"full_name":"Wakelam, Michael","last_name":"Wakelam","first_name":"Michael"},{"full_name":"Casanueva, Olivia","first_name":"Olivia","last_name":"Casanueva"}],"volume":19,"date_created":"2021-11-21T23:01:28Z","date_updated":"2023-08-14T11:53:27Z","article_number":"e3001431","file_date_updated":"2021-11-22T09:34:03Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000715818400001"],"pmid":["34723964"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pbio.3001431","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10322","intvolume":" 19","ddc":["570"],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","status":"public","oa_version":"Published Version","file":[{"file_id":"10330","relation":"main_file","date_created":"2021-11-22T09:34:03Z","date_updated":"2021-11-22T09:34:03Z","success":1,"checksum":"0c61b667f814fd9435b3ac42036fc36d","file_name":"2021_PLoSBio_Chauve.pdf","access_level":"open_access","creator":"cchlebak","file_size":4069215,"content_type":"application/pdf"}],"type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"citation":{"chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431.","short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, PLoS Biology 19 (2021).","mla":"Chauve, Laetitia, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H. J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021.","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 19(11), e3001431.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431"},"publication":"PLoS Biology","article_type":"original","date_published":"2021-11-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"date_updated":"2023-08-14T11:57:07Z","date_created":"2021-11-07T23:01:25Z","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201"}],"publisher":"Taylor and Francis","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","year":"2021","ec_funded":1,"file_date_updated":"2023-08-14T11:55:10Z","language":[{"iso":"eng"}],"doi":"10.1080/10586458.2021.1980459","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000710893500001"],"arxiv":["2007.07783"]},"publication_identifier":{"issn":["1058-6458"],"eissn":["1944-950X"]},"month":"10","file":[{"content_type":"application/pdf","file_size":1966019,"creator":"dernst","access_level":"open_access","file_name":"2023_ExperimentalMath_Akopyan.pdf","checksum":"3514382e3a1eb87fa6c61ad622874415","success":1,"date_updated":"2023-08-14T11:55:10Z","date_created":"2023-08-14T11:55:10Z","relation":"main_file","file_id":"14053"}],"oa_version":"Published Version","status":"public","ddc":["510"],"title":"The beauty of random polytopes inscribed in the 2-sphere","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10222","abstract":[{"lang":"eng","text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density."}],"type":"journal_article","date_published":"2021-10-25T00:00:00Z","page":"1-15","article_type":"original","citation":{"chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459.","short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459.","apa":"Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459","ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021.","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459"},"publication":"Experimental Mathematics","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1"},{"publication_status":"published","publisher":"Frontiers","department":[{"_id":"PaSc"}],"year":"2021","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","pmid":1,"date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T11:55:04Z","volume":8,"author":[{"full_name":"Sučec, Iva","last_name":"Sučec","first_name":"Iva"},{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"article_number":"762005","file_date_updated":"2021-11-23T15:06:58Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fmolb.2021.762005","month":"10","publication_identifier":{"eissn":["2296-889X"]},"title":"How do chaperones bind (partly) unfolded client proteins?","status":"public","ddc":["547"],"intvolume":" 8","_id":"10323","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"cchlebak","file_size":4700798,"content_type":"application/pdf","file_name":"2021_FrontiersMolBioSc_Sučec.pdf","access_level":"open_access","date_updated":"2021-11-23T15:06:58Z","date_created":"2021-11-23T15:06:58Z","success":1,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","file_id":"10333","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.","lang":"eng"}],"article_type":"original","publication":"Frontiers in Molecular Biosciences","citation":{"ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005."},"date_published":"2021-10-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10326","intvolume":" 7","status":"public","title":"Catabolism of strigolactones by a carboxylesterase","abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-11T00:00:00Z","citation":{"ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.","chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y."},"publication":"Nature Plants","page":"1495–1504 ","article_type":"original","article_processing_charge":"No","day":"11","scopus_import":"1","author":[{"full_name":"Xu, Enjun","first_name":"Enjun","last_name":"Xu"},{"last_name":"Chai","first_name":"Liang","full_name":"Chai, Liang"},{"full_name":"Zhang, Shiqi","first_name":"Shiqi","last_name":"Zhang"},{"first_name":"Ruixue","last_name":"Yu","full_name":"Yu, Ruixue"},{"full_name":"Zhang, Xixi","last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"last_name":"Xu","first_name":"Chongyi","full_name":"Xu, Chongyi"},{"first_name":"Yuxin","last_name":"Hu","full_name":"Hu, Yuxin"}],"volume":7,"date_updated":"2023-08-14T11:54:02Z","date_created":"2021-11-21T23:01:30Z","pmid":1,"acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","year":"2021","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","doi":"10.1038/s41477-021-01011-y","language":[{"iso":"eng"}],"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2055-0278"]},"month":"11"},{"date_created":"2023-05-23T16:40:56Z","date_updated":"2023-08-14T11:53:26Z","oa_version":"Published Version","author":[{"full_name":"Chauve, Laetitia","last_name":"Chauve","first_name":"Laetitia"},{"full_name":"Hodge, Francesca","first_name":"Francesca","last_name":"Hodge"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"full_name":"Masoudzadeh, Fatemah","last_name":"Masoudzadeh","first_name":"Fatemah"},{"full_name":"Mann, Harry-Jack","last_name":"Mann","first_name":"Harry-Jack"},{"full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo","first_name":"Andrea"},{"last_name":"Okkenhaug","first_name":"Hanneke","full_name":"Okkenhaug, Hanneke"},{"full_name":"West, Greg","first_name":"Greg","last_name":"West"},{"first_name":"Bebiana C.","last_name":"Sousa","full_name":"Sousa, Bebiana C."},{"first_name":"Anne","last_name":"Segonds-Pichon","full_name":"Segonds-Pichon, Anne"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"full_name":"Wingett, Steven","last_name":"Wingett","first_name":"Steven"},{"full_name":"Kienberger, Hermine","first_name":"Hermine","last_name":"Kienberger"},{"full_name":"Kleigrewe, Karin","last_name":"Kleigrewe","first_name":"Karin"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"},{"first_name":"Michael","last_name":"Wakelam","full_name":"Wakelam, Michael"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10322"}]},"ddc":["570"],"status":"public","title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","department":[{"_id":"MaDe"}],"publisher":"Zenodo","_id":"13069","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","abstract":[{"lang":"eng","text":"To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal."}],"type":"research_data_reference","doi":"10.5281/ZENODO.5519410","date_published":"2021-12-25T00:00:00Z","citation":{"short":"L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).","mla":"Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410.","chicago":"Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.","ama":"Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410","ieee":"L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021.","apa":"Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410","ista":"Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5547464","open_access":"1"}],"oa":1,"month":"12","day":"25","article_processing_charge":"No"},{"author":[{"last_name":"Zamyatin","first_name":"Alexei","full_name":"Zamyatin, Alexei"},{"first_name":"Mustafa","last_name":"Al-Bassam","full_name":"Al-Bassam, Mustafa"},{"last_name":"Zindros","first_name":"Dionysis","full_name":"Zindros, Dionysis"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"last_name":"Kiayias","first_name":"Aggelos","full_name":"Kiayias, Aggelos"},{"last_name":"Knottenbelt","first_name":"William J.","full_name":"Knottenbelt, William J."}],"volume":"12675 ","date_updated":"2023-08-14T12:59:26Z","date_created":"2021-11-21T23:01:29Z","acknowledgement":"We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.","year":"2021","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"],"issn":["0302-9743"],"eisbn":["978-3-662-64331-0"]},"month":"10","doi":"10.1007/978-3-662-64331-0_1","conference":{"name":"FC: Financial Cryptography","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"language":[{"iso":"eng"}],"external_id":{"isi":["000712016200001"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1128"}],"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","_id":"10325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"SoK: Communication across distributed ledgers","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2021-10-23T00:00:00Z","citation":{"ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36."},"publication":"25th International Conference on Financial Cryptography and Data Security","page":"3-36"},{"abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Brick: Asynchronous incentive-compatible payment channels","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10324","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2021-10-23T00:00:00Z","page":"209-230","citation":{"ista":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.","apa":"Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11","ieee":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.","ama":"Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11","chicago":"Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.","mla":"Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.","short":"Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230."},"publication":"25th International Conference on Financial Cryptography and Data Security","volume":"12675 ","date_created":"2021-11-21T23:01:29Z","date_updated":"2023-08-14T12:59:58Z","author":[{"last_name":"Avarikioti","first_name":"Zeta","full_name":"Avarikioti, Zeta"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"},{"last_name":"Zindros","first_name":"Dionysis","full_name":"Zindros, Dionysis"}],"department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","publication_identifier":{"eisbn":["978-3-662-64331-0"],"issn":["0302-9743"],"isbn":["9-783-6626-4330-3"],"eissn":["1611-3349"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-64331-0_11","conference":{"name":"FC: Financial Cryptography","end_date":"2021-03-05","start_date":"2021-03-01","location":"Virtual"},"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"external_id":{"isi":["000712016200011"],"arxiv":["1905.11360"]}},{"author":[{"full_name":"Lee, Jungmin","first_name":"Jungmin","last_name":"Lee"},{"first_name":"Andyna","last_name":"Vernet","full_name":"Vernet, Andyna"},{"full_name":"Gruber, Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","first_name":"Nathalie","last_name":"Gruber"},{"full_name":"Kready, Kasia M.","last_name":"Kready","first_name":"Kasia M."},{"full_name":"Burrill, Devin R.","last_name":"Burrill","first_name":"Devin R."},{"full_name":"Way, Jeffrey C.","first_name":"Jeffrey C.","last_name":"Way"},{"full_name":"Silver, Pamela A.","first_name":"Pamela A.","last_name":"Silver"}],"date_created":"2021-11-28T23:01:28Z","date_updated":"2023-08-14T13:01:38Z","volume":34,"year":"2021","acknowledgement":"This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support.","pmid":1,"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Oxford University Press","article_number":"gzab025","doi":"10.1093/protein/gzab025","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1093/protein/gzab025","open_access":"1"}],"oa":1,"external_id":{"isi":["000746596900001"],"pmid":["34725710"]},"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"issn":["1741-0126"],"eissn":["1741-0134"]},"oa_version":"Published Version","_id":"10363","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","intvolume":" 34","abstract":[{"text":"Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia.","lang":"eng"}],"type":"journal_article","date_published":"2021-11-01T00:00:00Z","publication":"Protein Engineering, Design and Selection","citation":{"ama":"Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025","ieee":"J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021.","apa":"Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025","ista":"Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025.","short":"J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021).","mla":"Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025.","chicago":"Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1"},{"article_number":"203758","department":[{"_id":"CaHe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2021","volume":168,"date_updated":"2023-08-14T13:02:40Z","date_created":"2021-11-28T23:01:30Z","author":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"last_name":"Lennon","first_name":"Ana Maria","full_name":"Lennon, Ana Maria"},{"full_name":"Mayor, Roberto","first_name":"Roberto","last_name":"Mayor"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"}],"publication_identifier":{"issn":["2667-2901"]},"month":"11","quality_controlled":"1","isi":1,"external_id":{"isi":["000974771600028"],"pmid":["34800748"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cdev.2021.203758","type":"journal_article","issue":"12","intvolume":" 168","title":"Special rebranding issue: “Quantitative cell and developmental biology”","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10366","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"17","article_type":"letter_note","citation":{"ama":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758","ista":"Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.","ieee":"C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.","apa":"Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758","mla":"Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","chicago":"Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758."},"publication":"Cells and Development","date_published":"2021-11-17T00:00:00Z"},{"article_number":"6830","file_date_updated":"2021-12-10T08:54:09Z","ec_funded":1,"year":"2021","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"author":[{"full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C"},{"last_name":"Kamenev","first_name":"Dmitrii","full_name":"Kamenev, Dmitrii"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"first_name":"Dominik C","last_name":"Fachet","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","full_name":"Fachet, Dominik C"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"last_name":"Hadjab","first_name":"Saida","full_name":"Hadjab, Saida"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13058"}]},"date_updated":"2023-08-14T13:18:46Z","date_created":"2021-12-05T23:01:40Z","volume":12,"month":"11","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["34819507"],"isi":["000722322900020"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1038/s41467-021-27135-5","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.","lang":"eng"}],"_id":"10402","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Theory of branching morphogenesis by local interactions and global guidance","status":"public","ddc":["573"],"intvolume":" 12","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10529","date_updated":"2021-12-10T08:54:09Z","date_created":"2021-12-10T08:54:09Z","checksum":"63c56ec75314a71e63e7dd2920b3c5b5","success":1,"file_name":"2021_NatComm_Ucar.pdf","access_level":"open_access","file_size":2303405,"content_type":"application/pdf","creator":"cchlebak"}],"scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5.","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5"},"article_type":"original","date_published":"2021-11-24T00:00:00Z"},{"volume":13043,"date_updated":"2023-08-14T13:07:46Z","date_created":"2021-12-05T23:01:42Z","author":[{"full_name":"Chakraborty, Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","first_name":"Suvradip"},{"first_name":"Stefan","last_name":"Dziembowski","full_name":"Dziembowski, Stefan"},{"full_name":"Gałązka, Małgorzata","last_name":"Gałązka","first_name":"Małgorzata"},{"full_name":"Lizurej, Tomasz","first_name":"Tomasz","last_name":"Lizurej"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Yeo, Michelle X","first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2021","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-90453-1_14","conference":{"end_date":"2021-11-11","location":"Raleigh, NC, United States","start_date":"2021-11-08","name":"TCC: Theory of Cryptography Conference"},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000728364000014"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1224"}],"oa":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"month":"11","oa_version":"Preprint","intvolume":" 13043","status":"public","title":"Trojan-resilience without cryptography","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10407","abstract":[{"text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2021-11-04T00:00:00Z","page":"397-428","citation":{"ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14","ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14","mla":"Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14."},"article_processing_charge":"No","day":"04","scopus_import":"1"},{"month":"11","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.65954","isi":1,"quality_controlled":"1","external_id":{"isi":["000715789500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2021-12-10T08:31:41Z","article_number":"e65954","date_updated":"2023-08-14T13:12:07Z","date_created":"2021-12-05T23:01:40Z","volume":10,"author":[{"last_name":"Biane","first_name":"Celia","full_name":"Biane, Celia"},{"full_name":"Rückerl, Florian","first_name":"Florian","last_name":"Rückerl"},{"full_name":"Abrahamsson, Therese","first_name":"Therese","last_name":"Abrahamsson"},{"last_name":"Saint-Cloment","first_name":"Cécile","full_name":"Saint-Cloment, Cécile"},{"full_name":"Mariani, Jean","first_name":"Jean","last_name":"Mariani"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"first_name":"David A.","last_name":"Digregorio","full_name":"Digregorio, David A."},{"full_name":"Sherrard, Rachel M.","last_name":"Sherrard","first_name":"Rachel M."},{"full_name":"Cathala, Laurence","last_name":"Cathala","first_name":"Laurence"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"}],"acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","year":"2021","day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-03T00:00:00Z","article_type":"original","publication":"eLife","citation":{"chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954.","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954.","apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021.","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954"},"abstract":[{"lang":"eng","text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10528","date_updated":"2021-12-10T08:31:41Z","date_created":"2021-12-10T08:31:41Z","checksum":"c7c33c3319428d56e332e22349c50ed3","success":1,"file_name":"2021_eLife_Biane.pdf","access_level":"open_access","content_type":"application/pdf","file_size":13131322,"creator":"cchlebak"}],"status":"public","ddc":["570"],"title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","intvolume":" 10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10403"},{"language":[{"iso":"eng"}],"doi":"10.1038/s42005-021-00753-7","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["10.1038/s42005-021-00753-7"],"arxiv":["2101.02020"]},"month":"11","publication_identifier":{"eissn":["23993650"]},"date_created":"2021-12-05T23:01:39Z","date_updated":"2023-08-14T13:04:34Z","volume":4,"author":[{"full_name":"Barfknecht, Rafael E.","last_name":"Barfknecht","first_name":"Rafael E."},{"full_name":"Foerster, Angela","first_name":"Angela","last_name":"Foerster"},{"last_name":"Zinner","first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T."},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Springer Nature","year":"2021","acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","file_date_updated":"2021-12-06T14:53:41Z","ec_funded":1,"article_number":"252","date_published":"2021-11-26T00:00:00Z","article_type":"original","publication":"Communications Physics","citation":{"short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7.","chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7.","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021.","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252."},"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"alisjak","file_size":1068984,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_NatComm_Barfknecht.pdf","success":1,"checksum":"9097319952cb9a3d96e7fd3aa9813a03","date_created":"2021-12-06T14:53:41Z","date_updated":"2021-12-06T14:53:41Z","file_id":"10420","relation":"main_file"}],"status":"public","title":"Generation of spin currents by a temperature gradient in a two-terminal device","ddc":["530"],"intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10401","abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"issue":"1","type":"journal_article"},{"month":"11","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"doi":"10.1111/cgf.14418","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2110.07667"}],"external_id":{"isi":["000722952000024"],"arxiv":["2110.07667"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"author":[{"last_name":"Sietzen","first_name":"Stefan","full_name":"Sietzen, Stefan"},{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"first_name":"Judy","last_name":"Borowski","full_name":"Borowski, Judy"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"first_name":"Manuela","last_name":"Waldner","full_name":"Waldner, Manuela"}],"date_updated":"2023-08-14T13:11:42Z","date_created":"2021-12-05T23:01:40Z","volume":40,"year":"2021","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Wiley","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2021-11-27T00:00:00Z","publication":"Computer Graphics Forum","citation":{"chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418.","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418"},"article_type":"original","page":"253-264","abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10404","status":"public","title":"Interactive analysis of CNN robustness","intvolume":" 40"}]