[{"article_number":"19238","file_date_updated":"2021-10-05T14:56:48Z","license":"https://creativecommons.org/licenses/by/4.0/","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,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"author":[{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"full_name":"Stojanov, Miloš","first_name":"Miloš","last_name":"Stojanov"},{"full_name":"Blum, Sabine","first_name":"Sabine","last_name":"Blum"},{"full_name":"Baud, David","first_name":"David","last_name":"Baud"}],"date_created":"2021-10-03T22:01:21Z","date_updated":"2023-08-14T07:05:15Z","volume":11,"month":"09","publication_identifier":{"eissn":["2045-2322"]},"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":["000701575500083"],"pmid":["34584125"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-021-98411-z","language":[{"iso":"eng"}],"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."}],"_id":"10069","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["618"],"title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","intvolume":" 11","oa_version":"Published Version","file":[{"file_id":"10091","relation":"main_file","date_updated":"2021-10-05T14:56:48Z","date_created":"2021-10-05T14:56:48Z","success":1,"checksum":"f002ec22f609f58e1263b79e7f79601e","file_name":"2021_ScientificReports_Robinson.pdf","access_level":"open_access","creator":"cchlebak","file_size":6970368,"content_type":"application/pdf"}],"scopus_import":"1","day":"28","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Scientific Reports","citation":{"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","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.","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","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.","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","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."},"article_type":"original","date_published":"2021-09-28T00:00:00Z"},{"doi":"10.1038/s41586-021-03938-w","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2104.00653"],"isi":["000706977400002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.00653"}],"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":["1476-4687"],"issn":["0028-0836"]},"month":"09","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-021-04181-z"}]},"author":[{"full_name":"Zhou, Haoxin","last_name":"Zhou","first_name":"Haoxin"},{"last_name":"Xie","first_name":"Tian","full_name":"Xie, Tian"},{"last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"first_name":"Tobias","last_name":"Holder","full_name":"Holder, Tobias"},{"full_name":"Ehrets, James R.","last_name":"Ehrets","first_name":"James R."},{"last_name":"Spanton","first_name":"Eric M.","full_name":"Spanton, Eric M."},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."}],"date_created":"2021-09-19T22:01:25Z","date_updated":"2023-08-14T07:04:06Z","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","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"date_published":"2021-09-01T00:00:00Z","citation":{"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.","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."},"publication":"Nature","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["condensed matter - mesoscale and nanoscale physics","condensed matter - strongly correlated electrons","multidisciplinary"],"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10025","title":"Half and quarter metals in rhombohedral trilayer graphene","status":"public","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"},{"article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2021-09-17T00:00:00Z","page":"431-450","citation":{"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.","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."},"publication":"FC 2021 Workshops","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"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"Reactive key-loss protection in blockchains","_id":"10076","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-6626-3957-3"],"issn":["0302-9743"],"eisbn":["978-3-662-63958-0"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-63958-0_34","conference":{"name":"FC: International Conference on Financial Cryptography and Data Security","end_date":"2021-03-05","location":"Virtual","start_date":"2021-03-01"},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/"}],"oa":1,"external_id":{"isi":["000713005000034"]},"volume":"12676 ","date_updated":"2023-08-14T07:06:16Z","date_created":"2021-10-03T22:01:24Z","author":[{"last_name":"Blackshear","first_name":"Sam","full_name":"Blackshear, Sam"},{"last_name":"Chalkias","first_name":"Konstantinos","full_name":"Chalkias, Konstantinos"},{"last_name":"Chatzigiannis","first_name":"Panagiotis","full_name":"Chatzigiannis, Panagiotis"},{"full_name":"Faizullabhoy, Riyaz","last_name":"Faizullabhoy","first_name":"Riyaz"},{"full_name":"Khaburzaniya, Irakliy","first_name":"Irakliy","last_name":"Khaburzaniya"},{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Lind","first_name":"Joshua","full_name":"Lind, Joshua"},{"full_name":"Wong, David","first_name":"David","last_name":"Wong"},{"full_name":"Zakian, Tim","last_name":"Zakian","first_name":"Tim"}],"department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","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."},{"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10070","title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","status":"public","intvolume":" 281","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."}],"issue":"11","type":"journal_article","date_published":"2021-09-15T00:00:00Z","publication":"Journal of Functional Analysis","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.","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","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.","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"},"article_type":"original","day":"15","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870"},{"last_name":"Suzuki","first_name":"Kohei","full_name":"Suzuki, Kohei"}],"date_created":"2021-10-03T22:01:21Z","date_updated":"2023-08-14T07:05:44Z","volume":281,"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","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JaMa"}],"ec_funded":1,"article_number":"109234","doi":"10.1016/j.jfa.2021.109234","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2008.01492"],"isi":["000703896600005"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"quality_controlled":"1","isi":1,"project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"month":"09","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]}},{"month":"12","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"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":["000709899300001"],"pmid":["34626034"]},"quality_controlled":"1","isi":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"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"}],"doi":"10.1002/adma.202106858","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"article_number":"2106858","file_date_updated":"2022-02-03T13:16:14Z","ec_funded":1,"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,"publication_status":"published","publisher":"Wiley","department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"author":[{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu"},{"orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano","full_name":"Calcabrini, Mariano"},{"last_name":"Yu","first_name":"Yuan","full_name":"Yu, Yuan"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo"},{"last_name":"Kleinhanns","first_name":"Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias"},{"first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"first_name":"Oana","last_name":"Cojocaru‐Mirédin","full_name":"Cojocaru‐Mirédin, Oana"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"}],"related_material":{"record":[{"id":"12885","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-08-14T07:25:27Z","date_created":"2021-10-11T20:07:24Z","volume":33,"scopus_import":"1","keyword":["mechanical engineering","mechanics of materials","general materials science"],"day":"29","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Advanced Materials","citation":{"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","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.","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","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.","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).","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.","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."},"article_type":"original","date_published":"2021-12-29T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"52","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10123","status":"public","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","ddc":["620"],"intvolume":" 33","oa_version":"Published Version","file":[{"date_updated":"2022-02-03T13:16:14Z","date_created":"2022-02-03T13:16:14Z","success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","file_id":"10720","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":5595666,"file_name":"2021_AdvancedMaterials_Liu.pdf","access_level":"open_access"}]},{"issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2021-10-11T12:20:58Z","date_updated":"2021-10-11T12:20:58Z","success":1,"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_id":"10121","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":1680010,"file_name":"2021_JBC_Artan.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10117","intvolume":" 297","ddc":["612"],"status":"public","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","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.","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","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."},"publication":"Journal of Biological Chemistry","article_type":"original","ec_funded":1,"file_date_updated":"2021-10-11T12:20:58Z","article_number":"101094","author":[{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan"},{"full_name":"Barratt, Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","last_name":"Barratt","first_name":"Stephen"},{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"full_name":"Begum, Farida","first_name":"Farida","last_name":"Begum"},{"full_name":"Skehel, Mark","last_name":"Skehel","first_name":"Mark"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"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","year":"2021","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).","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"publisher":"Elsevier","publication_status":"published","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"month":"09","doi":"10.1016/J.JBC.2021.101094","language":[{"iso":"eng"}],"external_id":{"isi":["000706409200006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1"},{"intvolume":" 12974","ddc":["005"],"title":"Differential monitoring","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10108","oa_version":"Preprint","file":[{"relation":"main_file","file_id":"10109","date_created":"2021-10-07T23:32:18Z","date_updated":"2021-10-07T23:32:18Z","checksum":"554c7fdb259eda703a8b6328a6dad55a","success":1,"file_name":"differentialmonitoring-cameraready-openaccess.pdf","access_level":"open_access","file_size":350632,"content_type":"application/pdf","creator":"fmuehlbo"}],"alternative_title":["LNCS"],"type":"conference","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."}],"page":"231-243","citation":{"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","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","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."},"publication":"International Conference on Runtime Verification","date_published":"2021-10-06T00:00:00Z","keyword":["run-time verification","software engineering","implicit specification"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","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.","volume":12974,"date_created":"2021-10-07T23:30:10Z","date_updated":"2023-08-14T07:20:30Z","related_material":{"record":[{"relation":"extended_version","status":"public","id":"9946"}]},"author":[{"full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"place":"Cham","file_date_updated":"2021-10-07T23:32:18Z","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000719383800012"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-88494-9_12","conference":{"name":"RV: Runtime Verification","start_date":"2021-10-11","location":"Virtual","end_date":"2021-10-14"},"publication_identifier":{"isbn":["978-3-030-88493-2"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-88494-9"]},"month":"10"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10116","ddc":["610"],"title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","status":"public","intvolume":" 10","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_eLife_VuongBrender.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":1774624,"file_id":"10122","relation":"main_file","success":1,"checksum":"b465e172d2b1f57aa26a2571a085d052","date_created":"2021-10-11T14:15:07Z","date_updated":"2021-10-11T14:15:07Z"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"eLife","citation":{"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.","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).","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","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"},"article_type":"original","date_published":"2021-09-17T00:00:00Z","scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"No","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).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Vuong-Brender, Thanh","last_name":"Vuong-Brender","first_name":"Thanh","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E"},{"first_name":"Sean","last_name":"Flynn","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","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-10-10T22:01:22Z","date_updated":"2023-08-14T07:23:39Z","volume":10,"article_number":"e68238","file_date_updated":"2021-10-11T14:15:07Z","ec_funded":1,"external_id":{"isi":["000695716100001"],"pmid":["34499028"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.7554/eLife.68238","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2050-084X"]}},{"day":"17","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["virology","infectious diseases"],"date_published":"2021-09-17T00:00:00Z","publication":"Viruses","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.","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.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","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.","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","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"},"article_type":"original","abstract":[{"lang":"eng","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."}],"issue":"9","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_Viruses_Obr.pdf","file_size":4146796,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10115","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","success":1,"date_updated":"2021-10-08T10:38:15Z","date_created":"2021-10-08T10:38:15Z"}],"oa_version":"Published Version","_id":"10103","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","ddc":["616"],"intvolume":" 13","month":"09","publication_identifier":{"issn":["1999-4915"]},"doi":"10.3390/v13091853","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":["000699841100001"],"pmid":["34578434"]},"isi":1,"quality_controlled":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"file_date_updated":"2021-10-08T10:38:15Z","article_number":"1853","author":[{"orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin","full_name":"Obr, Martin"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."}],"date_updated":"2023-08-14T07:21:51Z","date_created":"2021-10-07T09:13:29Z","volume":13,"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"MDPI"},{"oa":1,"external_id":{"arxiv":["2107.05735"],"isi":["000704414400002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.05735"}],"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"doi":"10.1103/physrevb.104.104205","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"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","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"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"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"date_updated":"2023-08-14T07:24:47Z","date_created":"2021-10-02T09:03:42Z","volume":104,"article_number":"104205","ec_funded":1,"publication":"Physical Review B","citation":{"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.","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.","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","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."},"article_type":"original","date_published":"2021-09-30T00:00:00Z","day":"30","article_processing_charge":"No","_id":"10067","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Entanglement transitions from restricted Boltzmann machines","intvolume":" 104","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"10"},{"date_published":"2021-09-01T00:00:00Z","page":"17","citation":{"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.","ama":"Mühlböck F, Henzinger TA. 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.","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."},"has_accepted_license":"1","article_processing_charge":"No","day":"01","keyword":["run-time verification","software engineering","implicit specification"],"oa_version":"Published Version","file":[{"file_name":"differentialmonitoring-techreport.pdf","access_level":"open_access","creator":"fmuehlbo","file_size":"320453","content_type":"application/pdf","file_id":"9948","relation":"main_file","date_created":"2021-08-20T19:59:44Z","date_updated":"2021-09-03T12:34:28Z","checksum":"0f9aafd59444cb6bdca6925d163ab946"}],"ddc":["005"],"title":"Differential monitoring","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"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","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:9946","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"publication_identifier":{"issn":["2664-1690"]},"month":"09","date_created":"2021-08-20T20:00:37Z","date_updated":"2023-08-14T07:20:29Z","related_material":{"record":[{"relation":"other","status":"public","id":"9281"},{"relation":"shorter_version","status":"public","id":"10108"}]},"author":[{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"publisher":"IST Austria","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2021","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.","file_date_updated":"2021-09-03T12:34:28Z"},{"date_published":"2021-09-19T00:00:00Z","article_type":"original","citation":{"ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416","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","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).","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."},"publication":"Materials","article_processing_charge":"Yes","has_accepted_license":"1","day":"19","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":4404141,"content_type":"application/pdf","file_name":"2021_Materials_Chang.pdf","access_level":"open_access","date_created":"2021-10-14T11:56:39Z","date_updated":"2021-10-14T11:56:39Z","success":1,"checksum":"4929dfc673a3ae77c010b6174279cc1d","file_id":"10140","relation":"main_file"}],"intvolume":" 14","title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","ddc":["540"],"status":"public","_id":"10073","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"18","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.3390/ma14185416","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34576640"],"isi":["000700689400001"]},"publication_identifier":{"eissn":["1996-1944"]},"month":"09","volume":14,"date_created":"2021-10-03T22:01:23Z","date_updated":"2023-08-14T08:00:01Z","author":[{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"}],"department":[{"_id":"MaIb"}],"publisher":"MDPI","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","file_date_updated":"2021-10-14T11:56:39Z","article_number":"5416"},{"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"month":"06","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/molbev/msab178","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"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":["34146097"],"isi":["000741368600009"]},"file_date_updated":"2022-05-06T09:47:18Z","date_created":"2021-10-21T07:49:12Z","date_updated":"2023-08-14T08:03:06Z","author":[{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","last_name":"Moldovan","first_name":"Mikhail A.","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press ","publication_status":"published","pmid":1,"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","article_processing_charge":"No","has_accepted_license":"1","day":"19","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"scopus_import":"1","date_published":"2021-06-19T00:00:00Z","article_type":"original","citation":{"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.","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","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.","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","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.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","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."},"publication":"Molecular Biology and Evolution","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":1008594,"creator":"dernst","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","access_level":"open_access","date_updated":"2022-05-06T09:47:18Z","date_created":"2022-05-06T09:47:18Z","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","success":1,"relation":"main_file","file_id":"11352"}],"oa_version":"Published Version","status":"public","title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","ddc":["610"],"_id":"10167","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"1","status":"public","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","ddc":["610"],"intvolume":" 12","_id":"10163","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":5111706,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_NatComm_Appel.pdf","checksum":"d99fcd51aebde19c21314e3de0148007","success":1,"date_created":"2021-10-21T13:51:49Z","date_updated":"2021-10-21T13:51:49Z","relation":"main_file","file_id":"10169"}],"oa_version":"Published Version","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"day":"19","has_accepted_license":"1","article_processing_charge":"No","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.","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.","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","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)."},"date_published":"2021-10-19T00:00:00Z","article_number":"6078","file_date_updated":"2021-10-21T13:51:49Z","publication_status":"published","department":[{"_id":"CaBe"}],"publisher":"Springer Nature","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.","year":"2021","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","first_name":"Vedran","last_name":"Franke"},{"full_name":"Bruno, Melania","last_name":"Bruno","first_name":"Melania"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"full_name":"Kasiliauskaite, Aiste","last_name":"Kasiliauskaite","first_name":"Aiste"},{"last_name":"Kaufmann","first_name":"Tanja","full_name":"Kaufmann, Tanja"},{"full_name":"Schoeberl, Ursula E.","first_name":"Ursula E.","last_name":"Schoeberl"},{"last_name":"Puchinger","first_name":"Martin G.","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","first_name":"Sebastian","last_name":"Kostrhon"},{"last_name":"Ebenwaldner","first_name":"Carmen","full_name":"Ebenwaldner, Carmen"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"full_name":"Beltzung, Etienne","first_name":"Etienne","last_name":"Beltzung"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"last_name":"Lin","first_name":"Gen","full_name":"Lin, Gen"},{"full_name":"Vlasova, Anna","last_name":"Vlasova","first_name":"Anna"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"},{"full_name":"Pavri, Rushad","last_name":"Pavri","first_name":"Rushad"},{"last_name":"Stark","first_name":"Alexander","full_name":"Stark, Alexander"},{"full_name":"Akalin, Altuna","last_name":"Akalin","first_name":"Altuna"},{"first_name":"Richard","last_name":"Stefl","full_name":"Stefl, Richard"},{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036"},{"last_name":"Djinovic-Carugo","first_name":"Kristina","full_name":"Djinovic-Carugo, Kristina"},{"first_name":"Dea","last_name":"Slade","full_name":"Slade, Dea"}],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version","description":"Preprint "}]},"month":"10","publication_identifier":{"eissn":["2041-1723"]},"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":{"isi":["000709050300001"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-021-26360-2"},{"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1111/cgf.142626","project":[{"name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000657959600017"]},"oa":1,"ec_funded":1,"file_date_updated":"2021-10-11T12:06:50Z","volume":40,"date_updated":"2023-08-14T08:01:50Z","date_created":"2021-06-13T22:01:32Z","author":[{"last_name":"Rittig","first_name":"Tobias","full_name":"Rittig, Tobias"},{"first_name":"Denis","last_name":"Sumin","full_name":"Sumin, Denis"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Voloboy, Alexey","first_name":"Alexey","last_name":"Voloboy"},{"last_name":"Wilkie","first_name":"Alexander","full_name":"Wilkie, Alexander"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"},{"full_name":"Weyrich, Tim","first_name":"Tim","last_name":"Weyrich"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"publisher":"Wiley","department":[{"_id":"BeBi"}],"publication_status":"published","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).","year":"2021","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-05-01T00:00:00Z","page":"205-219","article_type":"original","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","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","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.","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.","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.","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."},"publication":"Computer Graphics Forum","issue":"2","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"}],"type":"journal_article","file":[{"success":1,"checksum":"33271724215f54a75c39d2ed40f2c502","date_created":"2021-10-11T12:06:50Z","date_updated":"2021-10-11T12:06:50Z","file_id":"10120","relation":"main_file","creator":"bbickel","content_type":"application/pdf","file_size":26026501,"access_level":"open_access","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf"}],"oa_version":"Submitted Version","intvolume":" 40","status":"public","title":"Neural acceleration of scattering-aware color 3D printing","ddc":["004"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9547"},{"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"NanoFab"}],"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).","date_created":"2021-10-24T22:01:33Z","date_updated":"2023-08-14T08:04:42Z","volume":7,"author":[{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"last_name":"Voronin","first_name":"Kirill V.","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ma","first_name":"Weiliang","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","first_name":"Qiaoliang","last_name":"Bao"},{"full_name":"Volkov, Valentyn S.","first_name":"Valentyn S.","last_name":"Volkov"},{"last_name":"Hillenbrand","first_name":"Rainer","full_name":"Hillenbrand, Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"article_number":"abj0127","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-10-27T14:16:06Z","isi":1,"quality_controlled":"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":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abj0127","month":"10","publication_identifier":{"eissn":["23752548"]},"ddc":["530"],"status":"public","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","intvolume":" 7","_id":"10177","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"10189","relation":"main_file","date_updated":"2021-10-27T14:16:06Z","date_created":"2021-10-27T14:16:06Z","success":1,"checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":2441163}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"41","article_type":"original","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.","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).","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.","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","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.","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.","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"},"date_published":"2021-10-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"Yes","has_accepted_license":"1"},{"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":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000704581600001"],"pmid":["34616041"]},"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/","description":"News on IST Webpage","relation":"press_release"}]},"author":[{"last_name":"Vercellino","first_name":"Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"LeSa"}],"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","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.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","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.","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.","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","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","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","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","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10146"},{"scopus_import":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"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","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.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","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","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.","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."},"publication":"Journal of Mathematical Physics","date_published":"2021-10-01T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"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.","lang":"eng"}],"intvolume":" 62","status":"public","title":"Topological field theory on r-spin surfaces and the Arf-invariant","_id":"10176","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","publication_identifier":{"issn":["00222488"]},"month":"10","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1802.09978"],"isi":["000755638500010"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.09978"}],"language":[{"iso":"eng"}],"doi":"10.1063/5.0037826","article_number":"102302","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","publication_status":"published","year":"2021","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.”","volume":62,"date_updated":"2023-08-14T08:04:12Z","date_created":"2021-10-24T22:01:32Z","author":[{"first_name":"Ingo","last_name":"Runkel","full_name":"Runkel, Ingo"},{"id":"7943226E-220E-11EA-94C7-D59F3DDC885E","orcid":"0000-0003-2834-5054","first_name":"Lorant","last_name":"Szegedy","full_name":"Szegedy, Lorant"}]},{"type":"journal_article","issue":"23","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"}],"intvolume":" 40","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","ddc":["610"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10179","oa_version":"Published Version","file":[{"success":1,"checksum":"78d2d02e775322297e774f72810a41a4","date_updated":"2021-12-13T14:54:14Z","date_created":"2021-12-13T14:54:14Z","file_id":"10541","relation":"main_file","creator":"alisjak","content_type":"application/pdf","file_size":7819881,"access_level":"open_access","file_name":"2021_EMBO_Bajaj.pdf"}],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"18","article_type":"original","citation":{"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).","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.","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.","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","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","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","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."},"publication":"EMBO Journal","date_published":"2021-10-18T00:00:00Z","article_number":"e108714","file_date_updated":"2021-12-13T14:54:14Z","publisher":"Embo Press","department":[{"_id":"Bio"}],"publication_status":"published","pmid":1,"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).","volume":40,"date_updated":"2023-08-14T08:05:23Z","date_created":"2021-10-24T22:01:34Z","author":[{"first_name":"Sunanjay","last_name":"Bajaj","full_name":"Bajaj, Sunanjay"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"first_name":"Abel","last_name":"Vertesy","full_name":"Vertesy, Abel"},{"last_name":"Nagumo Wong","first_name":"Sakurako","full_name":"Nagumo Wong, Sakurako"},{"full_name":"Krenn, Veronica","last_name":"Krenn","first_name":"Veronica"},{"full_name":"Lévi-Strauss, Julie","first_name":"Julie","last_name":"Lévi-Strauss"},{"last_name":"Knoblich","first_name":"Juergen A.","full_name":"Knoblich, Juergen A."}],"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"month":"10","quality_controlled":"1","isi":1,"external_id":{"pmid":["34661293"],"isi":["000708012800001"]},"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":"10.15252/embj.2021108714"},{"file_date_updated":"2021-11-03T11:31:24Z","article_number":"6063","author":[{"full_name":"Sortino, Luca","first_name":"Luca","last_name":"Sortino"},{"full_name":"Zotev, Panaiot G.","first_name":"Panaiot G.","last_name":"Zotev"},{"first_name":"Catherine L.","last_name":"Phillips","full_name":"Phillips, Catherine L."},{"full_name":"Brash, Alistair J.","first_name":"Alistair J.","last_name":"Brash"},{"first_name":"Javier","last_name":"Cambiasso","full_name":"Cambiasso, Javier"},{"last_name":"Marensi","first_name":"Elena","orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena"},{"last_name":"Fox","first_name":"A. Mark","full_name":"Fox, A. Mark"},{"full_name":"Maier, Stefan A.","first_name":"Stefan A.","last_name":"Maier"},{"full_name":"Sapienza, Riccardo","first_name":"Riccardo","last_name":"Sapienza"},{"first_name":"Alexander I.","last_name":"Tartakovskii","full_name":"Tartakovskii, Alexander I."}],"date_created":"2021-10-31T23:01:30Z","date_updated":"2023-08-14T08:12:12Z","volume":12,"year":"2021","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.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"month":"10","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-021-26262-3","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":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"10212","checksum":"8580d128389860f732028c521cd5949e","success":1,"date_updated":"2021-11-03T11:31:24Z","date_created":"2021-11-03T11:31:24Z","access_level":"open_access","file_name":"2021_NatComm_Sortino.pdf","content_type":"application/pdf","file_size":1434201,"creator":"cchlebak"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10203","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","day":"18","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-10-18T00:00:00Z","publication":"Nature Communications","citation":{"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.","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","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.","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","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.","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).","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."},"article_type":"original"}]