[{"ec_funded":1,"status":"public","doi":"10.1098/rstb.2019.0528","quality_controlled":"1","volume":375,"abstract":[{"lang":"eng","text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed."}],"author":[{"last_name":"Kulmuni","full_name":"Kulmuni, Jonna","first_name":"Jonna"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Kay","last_name":"Lucek","full_name":"Lucek, Kay"},{"first_name":"Vincent","full_name":"Savolainen, Vincent","last_name":"Savolainen"},{"first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"publisher":"The Royal Society","article_number":"20190528","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"scopus_import":"1","type":"journal_article","publication_status":"published","oa_version":"Published Version","year":"2020","month":"07","isi":1,"article_type":"original","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","date_created":"2020-07-26T22:01:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       375","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","external_id":{"pmid":["32654637"],"isi":["000552662100001"]},"issue":"1806","citation":{"ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society Series B: Biological sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” <i>Philosophical Transactions of the Royal Society. Series B: Biological sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., &#38; Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>.","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>."},"oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-08-22T08:21:31Z","article_processing_charge":"No","day":"12","_id":"8168","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}],"pmid":1,"main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0528","open_access":"1"}],"date_published":"2020-07-12T00:00:00Z"},{"external_id":{"isi":["000552662100013"],"pmid":["32654641"]},"issue":"1806","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","intvolume":"       375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ieee":"H. Shang <i>et al.</i>, “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>","ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>.","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &#38; Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>."},"article_processing_charge":"No","day":"12","_id":"8169","date_updated":"2023-08-22T08:23:24Z","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"pmid":1,"date_published":"2020-07-12T00:00:00Z","quality_controlled":"1","volume":375,"doi":"10.1098/rstb.2019.0544","status":"public","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","publication_identifier":{"eissn":["14712970"]},"scopus_import":"1","abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"author":[{"first_name":"Huiying","full_name":"Shang, Huiying","last_name":"Shang"},{"first_name":"Jaqueline","last_name":"Hess","full_name":"Hess, Jaqueline"},{"first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Ingvarsson","full_name":"Ingvarsson, Pär K.","first_name":"Pär K."},{"full_name":"Liu, Jianquan","last_name":"Liu","first_name":"Jianquan"},{"last_name":"Lexer","full_name":"Lexer, Christian","first_name":"Christian"}],"article_number":"20190544","publisher":"The Royal Society","oa_version":"Published Version","type":"journal_article","publication_status":"published","article_type":"original","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","date_created":"2020-07-26T22:01:02Z","year":"2020","month":"07","isi":1},{"month":"07","isi":1,"year":"2020","date_created":"2020-07-26T22:01:02Z","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","arxiv":1,"article_type":"original","publication_status":"published","type":"journal_article","oa_version":"Preprint","publisher":"American Physical Society","author":[{"first_name":"Adam S.","full_name":"Chatterley, Adam S.","last_name":"Chatterley"},{"first_name":"Lars","full_name":"Christiansen, Lars","last_name":"Christiansen"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"full_name":"Jørgensen, Anders V.","last_name":"Jørgensen","first_name":"Anders V."},{"first_name":"Benjamin","last_name":"Shepperson","full_name":"Shepperson, Benjamin"},{"last_name":"Cherepanov","full_name":"Cherepanov, Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"full_name":"Bighin, Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo"},{"first_name":"Robert E.","last_name":"Zillich","full_name":"Zillich, Robert E."},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail"},{"full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt","first_name":"Henrik"}],"article_number":"013001","abstract":[{"lang":"eng","text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes."}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"scopus_import":"1","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","status":"public","ec_funded":1,"doi":"10.1103/PhysRevLett.125.013001","volume":125,"quality_controlled":"1","date_published":"2020-07-03T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}],"language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"date_updated":"2024-08-07T07:16:52Z","_id":"8170","day":"03","project":[{"grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"article_processing_charge":"No","citation":{"short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ieee":"A. S. Chatterley <i>et al.</i>, “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” <i>Physical Review Letters</i>, vol. 125, no. 1. American Physical Society, 2020.","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. 2020;125(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>.","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>"},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       125","publication":"Physical Review Letters","issue":"1","external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Photoswitching Proteins","intvolume":"      2173","status":"public","volume":2173,"doi":"10.1007/978-1-0716-0755-8_16","editor":[{"last_name":"Niopek","full_name":"Niopek, Dominik","first_name":"Dominik"}],"alternative_title":["Methods in Molecular Biology"],"abstract":[{"lang":"eng","text":"Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware."}],"publisher":"Springer Nature","author":[{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L"}],"page":"233-246","citation":{"ista":"Kainrath S, Janovjak HL. 2020.Design and application of light-regulated receptor tyrosine kinases. In: Photoswitching Proteins. Methods in Molecular Biology, vol. 2173, 233–246.","ama":"Kainrath S, Janovjak HL. Design and application of light-regulated receptor tyrosine kinases. In: Niopek D, ed. <i>Photoswitching Proteins</i>. Vol 2173. MIMB. Springer Nature; 2020:233-246. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>","short":"S. Kainrath, H.L. Janovjak, in:, D. Niopek (Ed.), Photoswitching Proteins, Springer Nature, 2020, pp. 233–246.","ieee":"S. Kainrath and H. L. Janovjak, “Design and application of light-regulated receptor tyrosine kinases,” in <i>Photoswitching Proteins</i>, vol. 2173, D. Niopek, Ed. Springer Nature, 2020, pp. 233–246.","apa":"Kainrath, S., &#38; Janovjak, H. L. (2020). Design and application of light-regulated receptor tyrosine kinases. In D. Niopek (Ed.), <i>Photoswitching Proteins</i> (Vol. 2173, pp. 233–246). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>","mla":"Kainrath, Stephanie, and Harald L. Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” <i>Photoswitching Proteins</i>, edited by Dominik Niopek, vol. 2173, Springer Nature, 2020, pp. 233–46, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>.","chicago":"Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” In <i>Photoswitching Proteins</i>, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>."},"scopus_import":"1","publication_identifier":{"eissn":["19406029"],"eisbn":["9781071607558"]},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:17:17Z","department":[{"_id":"CaGu"}],"type":"book_chapter","series_title":"MIMB","publication_status":"published","article_processing_charge":"No","_id":"8173","day":"11","oa_version":"None","year":"2020","month":"07","date_published":"2020-07-11T00:00:00Z","title":"Design and application of light-regulated receptor tyrosine kinases","date_created":"2020-07-26T22:01:03Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.15479/AT:ISTA:8181","publisher":"IST Austria","author":[{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert"}],"file_date_updated":"2020-08-24T15:43:52Z","oa":1,"citation":{"chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>.","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>","mla":"Hauschild, Robert. <i>Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","short":"R. Hauschild, (2020).","ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>"},"tmp":{"legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD","name":"The 3-Clause BSD License"},"date_updated":"2021-01-11T15:29:08Z","department":[{"_id":"Bio"}],"type":"software","license":"https://opensource.org/licenses/BSD-3-Clause","_id":"8181","day":"24","year":"2020","date_published":"2020-08-24T00:00:00Z","month":"08","file":[{"file_size":6577,"date_updated":"2020-08-24T15:43:49Z","relation":"main_file","success":1,"content_type":"text/plain","creator":"rhauschild","file_id":"8290","file_name":"centriolesDistance.m","access_level":"open_access","date_created":"2020-08-24T15:43:49Z","checksum":"878c60885ce30afb59a884dd5eef451c"},{"file_size":2680,"relation":"main_file","date_updated":"2020-08-24T15:43:52Z","access_level":"open_access","checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","date_created":"2020-08-24T15:43:52Z","content_type":"text/plain","success":1,"file_id":"8291","file_name":"goTracking.m","creator":"rhauschild"}],"title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","has_accepted_license":"1","date_created":"2020-07-28T16:24:37Z"},{"file_date_updated":"2020-07-31T16:57:12Z","oa":1,"citation":{"ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2020:7498-7507. doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Virtual, 2020, pp. 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., &#38; Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 7498–7507). Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2020, pp. 7498–507, doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>.","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 7498–7507. IEEE, 2020. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>."},"page":"7498-7507","external_id":{"arxiv":["2004.04180"]},"publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_updated":"2020-07-31T16:57:12Z","file_size":10262773,"access_level":"open_access","date_created":"2020-07-31T16:57:12Z","file_id":"8187","file_name":"paper.pdf","creator":"phenders","success":1,"content_type":"application/pdf"}],"main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"date_published":"2020-07-01T00:00:00Z","article_processing_charge":"No","_id":"8186","day":"01","date_updated":"2023-10-17T07:37:11Z","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2020-06-14","end_date":"2020-06-19","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Virtual"},"scopus_import":"1","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"abstract":[{"lang":"eng","text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n  A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n  We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes."}],"author":[{"first_name":"Paul M","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Vagia","last_name":"Tsiminaki","full_name":"Tsiminaki, Vagia"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"publisher":"IEEE","quality_controlled":"1","doi":"10.1109/CVPR42600.2020.00752","ddc":["004"],"status":"public","arxiv":1,"title":"Leveraging 2D data to learn textured 3D mesh generation","has_accepted_license":"1","date_created":"2020-07-31T16:53:49Z","year":"2020","month":"07","oa_version":"Submitted Version","type":"conference","publication_status":"published"},{"date_published":"2020-07-07T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/2007.06705","open_access":"1"}],"_id":"8188","day":"07","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"date_updated":"2023-04-25T09:49:58Z","department":[{"_id":"ChLa"}],"citation":{"ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117.","short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 3106–3117.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 3106–3117.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Curran Associates; 2020:3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:3106–3117. Curran Associates, 2020.","apa":"Henderson, P. M., &#38; Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 3106–3117). Vancouver, Canada: Curran Associates.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Curran Associates, 2020, pp. 3106–3117."},"page":"3106–3117","oa":1,"external_id":{"arxiv":["2007.06705"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        33","publication":"34th Conference on Neural Information Processing Systems","date_created":"2020-07-31T16:59:19Z","title":"Unsupervised object-centric video generation and decomposition in 3D","arxiv":1,"month":"07","year":"2020","oa_version":"Preprint","publication_status":"published","type":"conference","publication_identifier":{"isbn":["9781713829546"]},"conference":{"start_date":"2020-12-06","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada"},"author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M","last_name":"Henderson","orcid":"0000-0002-5198-7445","first_name":"Paul M"},{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"publisher":"Curran Associates","abstract":[{"lang":"eng","text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking."}],"volume":33,"quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","status":"public"},{"volume":77,"quality_controlled":"1","doi":"10.1016/j.nanoen.2020.105116","status":"public","acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","scopus_import":"1","publication_identifier":{"issn":["2211-2855"]},"abstract":[{"text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface.","lang":"eng"}],"author":[{"last_name":"Yu","full_name":"Yu, Xiaoting","first_name":"Xiaoting"},{"full_name":"Liu, Junfeng","last_name":"Liu","first_name":"Junfeng"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"first_name":"Zhishan","full_name":"Luo, Zhishan","last_name":"Luo"},{"last_name":"Zuo","full_name":"Zuo, Yong","first_name":"Yong"},{"first_name":"Congcong","full_name":"Xing, Congcong","last_name":"Xing"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Nasiou, Déspina","last_name":"Nasiou","first_name":"Déspina"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Kai","full_name":"Pan, Kai","last_name":"Pan"},{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","first_name":"Tobias"},{"last_name":"Xie","full_name":"Xie, Ying","first_name":"Ying"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"article_number":"105116","publisher":"Elsevier","oa_version":"None","type":"journal_article","publication_status":"published","article_type":"original","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","date_created":"2020-08-02T22:00:57Z","year":"2020","month":"11","isi":1,"external_id":{"isi":["000581738300030"]},"issue":"11","intvolume":"        77","publication":"Nano Energy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. 2020;77(11). doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","ieee":"X. Yu <i>et al.</i>, “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” <i>Nano Energy</i>, vol. 77, no. 11. Elsevier, 2020.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>, vol. 77, no. 11, 105116, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>.","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>."},"article_processing_charge":"No","day":"01","_id":"8189","date_updated":"2023-08-22T08:24:05Z","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"date_published":"2020-11-01T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       219","publication":"The Journal of Cell Biology","issue":"8","external_id":{"isi":["000573631000004"]},"citation":{"ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"oa":1,"file_date_updated":"2021-02-02T23:30:03Z","language":[{"iso":"eng"}],"date_updated":"2023-10-17T10:04:49Z","department":[{"_id":"MiSi"}],"day":"22","_id":"8190","article_processing_charge":"No","date_published":"2020-07-22T00:00:00Z","file":[{"file_size":830725,"relation":"main_file","date_updated":"2021-02-02T23:30:03Z","access_level":"open_access","date_created":"2020-08-04T13:11:52Z","checksum":"30016d778d266b8e17d01094917873b8","embargo":"2021-02-01","content_type":"application/pdf","file_id":"8200","file_name":"2020_JCB_Sixt.pdf","creator":"dernst"}],"status":"public","ddc":["570"],"volume":219,"doi":"10.1083/jcb.202007029","author":[{"first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"Anna","full_name":"Huttenlocher, Anna","last_name":"Huttenlocher"}],"article_number":"e202007029","publisher":"Rockefeller University Press","publication_identifier":{"eissn":["1540-8140"]},"scopus_import":"1","publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","type":"journal_article","oa_version":"Published Version","isi":1,"month":"07","year":"2020","date_created":"2020-08-02T22:00:57Z","has_accepted_license":"1","title":"Zena Werb (1945-2020): Cell biology in context","article_type":"letter_note"},{"publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","external_id":{"isi":["000744436200004"]},"doi":"10.1145/3350755.3400213","quality_controlled":"1","issue":"7","abstract":[{"text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures.","lang":"eng"}],"publisher":"Association for Computing Machinery","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"},{"first_name":"Nandini","last_name":"Singhal","full_name":"Singhal, Nandini"}],"conference":{"start_date":"2020-07-15","end_date":"2020-07-17","location":"Virtual Event, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"scopus_import":"1","publication_identifier":{"isbn":["9781450369350"]},"citation":{"chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 37–49. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>.","apa":"Alistarh, D.-A., Brown, T. A., &#38; Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>","mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>.","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, Virtual Event, United States, 2020, no. 7, pp. 37–49.","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49.","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2020:37-49. doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>"},"page":"37-49","department":[{"_id":"DaAl"}],"date_updated":"2024-02-28T12:56:32Z","type":"conference","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","oa_version":"None","_id":"8191","day":"06","year":"2020","date_published":"2020-07-06T00:00:00Z","isi":1,"month":"07","date_created":"2020-08-02T22:00:58Z","title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures"},{"page":"48-56","citation":{"ieee":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, Nancy, France, 2020, vol. 30, pp. 48–56.","short":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","ista":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56.","ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020.","apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., &#38; Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i> (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","mla":"Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56."},"publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","intvolume":"        30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-06-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"8390","relation":"dissertation_contains"}]},"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T13:16:18Z","language":[{"iso":"eng"}],"project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"day":"01","_id":"8193","article_processing_charge":"No","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Karkhanis, Deep","last_name":"Karkhanis","first_name":"Deep"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr","first_name":"Petr"},{"first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705"}],"publisher":"Association for the Advancement of Artificial Intelligence","abstract":[{"text":"Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach.","lang":"eng"}],"publication_identifier":{"issn":["23340835"],"eissn":["23340843"]},"scopus_import":"1","conference":{"start_date":"2020-10-26","end_date":"2020-10-30","location":"Nancy, France","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"status":"public","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y.","quality_controlled":"1","volume":30,"month":"06","year":"2020","title":"Multiple-environment Markov decision processes: Efficient analysis and applications","date_created":"2020-08-02T22:00:58Z","publication_status":"published","type":"conference","oa_version":"None"},{"scopus_import":"1","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030510732"]},"conference":{"start_date":"2020-07-01","name":"IJCAR: International Joint Conference on Automated Reasoning","location":"Paris, France","end_date":"2020-07-04"},"publisher":"Springer Nature","author":[{"first_name":"Marek","last_name":"Baranowski","full_name":"Baranowski, Marek"},{"first_name":"Shaobo","last_name":"He","full_name":"He, Shaobo"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Nguyen","full_name":"Nguyen, Thanh Son","first_name":"Thanh Son"},{"full_name":"Rakamarić, Zvonimir","last_name":"Rakamarić","first_name":"Zvonimir"}],"abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"quality_controlled":"1","doi":"10.1007/978-3-030-51074-9_2","volume":12166,"status":"public","title":"An SMT theory of fixed-point arithmetic","date_created":"2020-08-02T22:00:59Z","isi":1,"month":"06","year":"2020","oa_version":"Published Version","publication_status":"published","type":"conference","oa":1,"page":"13-31","citation":{"chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In <i>Automated Reasoning</i>, 12166:13–31. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” <i>Automated Reasoning</i>, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., &#38; Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In <i>Automated Reasoning</i> (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in <i>Automated Reasoning</i>, Paris, France, 2020, vol. 12166, pp. 13–31.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: <i>Automated Reasoning</i>. Vol 12166. Springer Nature; 2020:13-31. doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>"},"alternative_title":["LNCS"],"external_id":{"isi":["000884318000002"]},"publication":"Automated Reasoning","intvolume":"     12166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-06-24T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1007/978-3-030-51074-9_2","open_access":"1"}],"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"_id":"8194","day":"24","article_processing_charge":"No","date_updated":"2023-08-22T08:27:25Z","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}]},{"related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"file":[{"access_level":"open_access","date_created":"2020-08-06T08:14:54Z","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"8201","file_name":"2020_LNCS_Kragl.pdf","file_size":804237,"relation":"main_file","date_updated":"2020-08-06T08:14:54Z"}],"date_published":"2020-07-14T00:00:00Z","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"day":"14","_id":"8195","article_processing_charge":"No","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","language":[{"iso":"eng"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: <i>Computer Aided Verification</i>. Vol 12224. Springer Nature; 2020:275-298. doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in <i>Computer Aided Verification</i>, 2020, vol. 12224, pp. 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” <i>Computer Aided Verification</i>, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2020). Refinement for structured concurrent programs. In <i>Computer Aided Verification</i> (Vol. 12224, pp. 275–298). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In <i>Computer Aided Verification</i>, 12224:275–98. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>."},"page":"275-298","file_date_updated":"2020-08-06T08:14:54Z","alternative_title":["LNCS"],"external_id":{"isi":["000695276000014"]},"publication":"Computer Aided Verification","intvolume":"     12224","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","date_created":"2020-08-03T11:45:35Z","title":"Refinement for structured concurrent programs","isi":1,"month":"07","year":"2020","oa_version":"Published Version","publication_status":"published","type":"conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030532871"],"eisbn":["9783030532888"],"issn":["0302-9743"]},"scopus_import":"1","author":[{"first_name":"Bernhard","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","abstract":[{"text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.","lang":"eng"}],"doi":"10.1007/978-3-030-53288-8_14","volume":12224,"quality_controlled":"1","ddc":["000"],"status":"public","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award)."},{"issue":"1","external_id":{"arxiv":["1903.04046"]},"publication":"Pure and Applied Analysis","intvolume":"         2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>.","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2020).  The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2020. <a href=\"https://doi.org/10.2140/paa.2020.2.35\">https://doi.org/10.2140/paa.2020.2.35</a>.","ama":"Lewin M, Lieb EH, Seiringer R.  The local density approximation in density functional theory. <i>Pure and Applied Analysis</i>. 2020;2(1):35-73. doi:<a href=\"https://doi.org/10.2140/paa.2020.2.35\">10.2140/paa.2020.2.35</a>","ista":"Lewin M, Lieb EH, Seiringer R. 2020.  The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation in density functional theory,” <i>Pure and Applied Analysis</i>, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73."},"page":"35-73","day":"01","_id":"14891","article_processing_charge":"No","date_updated":"2024-01-29T09:01:12Z","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"date_published":"2020-01-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1903.04046","open_access":"1"}],"volume":2,"doi":"10.2140/paa.2020.2.35","quality_controlled":"1","status":"public","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"scopus_import":"1","publisher":"Mathematical Sciences Publishers","author":[{"first_name":"Mathieu","full_name":"Lewin, Mathieu","last_name":"Lewin"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"abstract":[{"lang":"eng","text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"oa_version":"Preprint","publication_status":"published","type":"journal_article","date_created":"2024-01-28T23:01:44Z","title":" The local density approximation in density functional theory","arxiv":1,"article_type":"original","month":"01","year":"2020"},{"article_type":"original","date_created":"2024-02-28T08:50:34Z","title":"Molecular recognition at septin interfaces: The switches hold the key","year":"2020","month":"10","oa_version":"Published Version","type":"journal_article","publication_status":"published","publication_identifier":{"issn":["0022-2836"]},"abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"publisher":"Elsevier","author":[{"first_name":"Higor Vinícius Dias","full_name":"Rosa, Higor Vinícius Dias","last_name":"Rosa"},{"last_name":"Leonardo","full_name":"Leonardo, Diego Antonio","first_name":"Diego Antonio"},{"first_name":"Gabriel","full_name":"Brognara, Gabriel","last_name":"Brognara","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"last_name":"Brandão-Neto","full_name":"Brandão-Neto, José","first_name":"José"},{"full_name":"D'Muniz Pereira, Humberto","last_name":"D'Muniz Pereira","first_name":"Humberto"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"first_name":"Richard Charles","full_name":"Garratt, Richard Charles","last_name":"Garratt"}],"quality_controlled":"1","doi":"10.1016/j.jmb.2020.09.001","volume":432,"status":"public","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"date_published":"2020-10-02T00:00:00Z","article_processing_charge":"No","day":"02","_id":"15036","language":[{"iso":"eng"}],"date_updated":"2024-02-28T12:37:54Z","department":[{"_id":"MaLo"}],"page":"5784-5801","citation":{"mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801."},"oa":1,"external_id":{"pmid":["32910969"]},"issue":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Molecular Biology","intvolume":"       432","keyword":["Molecular Biology","Structural Biology"]},{"abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"publisher":"Elsevier","author":[{"last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette"},{"first_name":"Maximilian","full_name":"Schwihla, Maximilian","last_name":"Schwihla"},{"first_name":"Lucinda","last_name":"De-Araújo","full_name":"De-Araújo, Lucinda"},{"first_name":"Christina","last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lisa","full_name":"Jörg, Lisa","last_name":"Jörg"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"last_name":"Korbei","full_name":"Korbei, Barbara","first_name":"Barbara"}],"publication_identifier":{"issn":["1674-2052"]},"status":"public","ddc":["580"],"quality_controlled":"1","doi":"10.1016/j.molp.2020.02.012","volume":13,"year":"2020","month":"05","article_type":"original","date_created":"2024-02-28T08:55:56Z","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","has_accepted_license":"1","type":"journal_article","publication_status":"published","oa_version":"Published Version","file_date_updated":"2024-02-28T12:39:56Z","page":"717-731","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. 2020;13(5):717-731. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>","ieee":"J. Moulinier-Anzola <i>et al.</i>, “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” <i>Molecular Plant</i>, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Molecular Plant","keyword":["Plant Science","Molecular Biology"],"intvolume":"        13","external_id":{"pmid":["32087370"]},"issue":"5","pmid":1,"date_published":"2020-05-04T00:00:00Z","file":[{"checksum":"c538a5008f7827f62d17d40a3bfabe65","date_created":"2024-02-28T12:39:56Z","access_level":"open_access","content_type":"application/pdf","success":1,"creator":"dernst","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","file_id":"15038","file_size":3089212,"date_updated":"2024-02-28T12:39:56Z","relation":"main_file"}],"language":[{"iso":"eng"}],"date_updated":"2024-02-28T12:41:52Z","department":[{"_id":"EvBe"}],"article_processing_charge":"No","day":"04","_id":"15037"},{"keyword":["General Medicine"],"intvolume":"        34","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2002.12086"]},"issue":"06","oa":1,"citation":{"mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:<a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">10.1609/aaai.v34i06.6531</a>.","apa":"Brázdil, T., Chatterjee, K., Novotný, P., &#38; Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. New York, NY, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">https://doi.org/10.1609/aaai.v34i06.6531</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. Association for the Advancement of Artificial Intelligence, 2020. <a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">https://doi.org/10.1609/aaai.v34i06.6531</a>.","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>. 2020;34(06):9794-9801. doi:<a href=\"https://doi.org/10.1609/aaai.v34i06.6531\">10.1609/aaai.v34i06.6531</a>","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” <i>Proceedings of the 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020."},"page":"9794-9801","department":[{"_id":"KrCh"}],"date_updated":"2024-03-04T08:30:16Z","language":[{"iso":"eng"}],"article_processing_charge":"No","project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"_id":"15055","day":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.12086","open_access":"1"}],"date_published":"2020-04-03T00:00:00Z","status":"public","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","volume":34,"quality_controlled":"1","doi":"10.1609/aaai.v34i06.6531","abstract":[{"lang":"eng","text":"<jats:p>Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.</jats:p>"}],"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr"},{"full_name":"Vahala, Jiří","last_name":"Vahala","first_name":"Jiří"}],"publisher":"Association for the Advancement of Artificial Intelligence","conference":{"start_date":"2020-02-07","location":"New York, NY, United States","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence"},"publication_identifier":{"issn":["2374-3468"]},"type":"journal_article","publication_status":"published","oa_version":"Preprint","year":"2020","month":"04","article_type":"original","arxiv":1,"title":"Reinforcement learning of risk-constrained policies in Markov decision processes","date_created":"2024-03-04T08:07:22Z"},{"abstract":[{"text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.","lang":"eng"}],"author":[{"first_name":"Sangsoon","full_name":"Park, Sangsoon","last_name":"Park"},{"id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","first_name":"Murat"},{"first_name":"Seung Hyun","last_name":"Han","full_name":"Han, Seung Hyun"},{"first_name":"Hae-Eun H.","last_name":"Park","full_name":"Park, Hae-Eun H."},{"last_name":"Jung","full_name":"Jung, Yoonji","first_name":"Yoonji"},{"last_name":"Hwang","full_name":"Hwang, Ara B.","first_name":"Ara B."},{"full_name":"Shin, Won Sik","last_name":"Shin","first_name":"Won Sik"},{"first_name":"Kyong-Tai","last_name":"Kim","full_name":"Kim, Kyong-Tai"},{"first_name":"Seung-Jae V.","last_name":"Lee","full_name":"Lee, Seung-Jae V."}],"article_number":"aaw7824","publisher":"American Association for the Advancement of Science","publication_identifier":{"eissn":["2375-2548"]},"acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ","status":"public","ddc":["570"],"volume":6,"quality_controlled":"1","doi":"10.1126/sciadv.aaw7824","year":"2020","month":"07","article_type":"original","date_created":"2024-03-04T09:41:57Z","title":"VRK-1 extends life span by activation of AMPK via phosphorylation","has_accepted_license":"1","type":"journal_article","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","oa_version":"Published Version","file_date_updated":"2024-03-04T09:46:41Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"citation":{"short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).","ieee":"S. Park <i>et al.</i>, “VRK-1 extends life span by activation of AMPK via phosphorylation,” <i>Science Advances</i>, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824.","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. <i>Science Advances</i>. 2020;6(27). doi:<a href=\"https://doi.org/10.1126/sciadv.aaw7824\">10.1126/sciadv.aaw7824</a>","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” <i>Science Advances</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/sciadv.aaw7824\">https://doi.org/10.1126/sciadv.aaw7824</a>.","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aaw7824\">https://doi.org/10.1126/sciadv.aaw7824</a>","mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” <i>Science Advances</i>, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.aaw7824\">10.1126/sciadv.aaw7824</a>."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Science Advances","intvolume":"         6","issue":"27","date_published":"2020-07-01T00:00:00Z","file":[{"date_updated":"2024-03-04T09:46:41Z","relation":"main_file","file_size":1864415,"creator":"dernst","file_id":"15058","file_name":"2020_ScienceAdvances_Park.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","date_created":"2024-03-04T09:46:41Z"}],"language":[{"iso":"eng"}],"department":[{"_id":"MaDe"}],"date_updated":"2024-03-04T09:52:09Z","article_processing_charge":"No","day":"01","_id":"15057"},{"status":"public","acknowledgement":"This work has been financially supported by Comunidad de Madrid S2018/NMT-4333 ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects.","publication":"14th European Conference on Antennas and Propagation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.23919/eucap48036.2020.9135962","publisher":"IEEE","author":[{"first_name":"Michal","last_name":"Wasiak","full_name":"Wasiak, Michal"},{"last_name":"Botello","full_name":"Botello, Gabriel Santamaria","first_name":"Gabriel Santamaria"},{"first_name":"Kerlos Atia","full_name":"Abdalmalak, Kerlos Atia","last_name":"Abdalmalak"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Segovia-Vargas","full_name":"Segovia-Vargas, Daniel"},{"first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L.","last_name":"Schwefel"},{"last_name":"Munoz","full_name":"Munoz, Luis Enrique Garcia","first_name":"Luis Enrique Garcia"}],"abstract":[{"lang":"eng","text":"In this paper we present a room temperature radiometer that can eliminate the need of using cryostats in satellite payload reducing its weight and improving reliability. The proposed radiometer is based on an electro-optic upconverter that boosts up microwave photons energy by upconverting them into an optical domain what makes them immune to thermal noise even if operating at room temperature. The converter uses a high-quality factor whispering gallery\r\nmode (WGM) resonator providing naturally narrow bandwidth and therefore might be useful for applications like microwave hyperspectral sensing. The upconversion process is explained by\r\nproviding essential information about photon conversion efficiency and sensitivity. To prove the concept, we describe an experiment which shows state-of-the-art photon conversion efficiency n=10-5 per mW of pump power at the frequency of 80 GHz."}],"publication_identifier":{"eisbn":["9788831299008"]},"citation":{"chicago":"Wasiak, Michal, Gabriel Santamaria Botello, Kerlos Atia Abdalmalak, Florian Sedlmeir, Alfredo R Rueda Sanchez, Daniel Segovia-Vargas, Harald G. L. Schwefel, and Luis Enrique Garcia Munoz. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” In <i>14th European Conference on Antennas and Propagation</i>. IEEE, 2020. <a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">https://doi.org/10.23919/eucap48036.2020.9135962</a>.","apa":"Wasiak, M., Botello, G. S., Abdalmalak, K. A., Sedlmeir, F., Rueda Sanchez, A. R., Segovia-Vargas, D., … Munoz, L. E. G. (2020). Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In <i>14th European Conference on Antennas and Propagation</i>. Copenhagen, Denmark: IEEE. <a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">https://doi.org/10.23919/eucap48036.2020.9135962</a>","mla":"Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic Radiometer for Cubesats.” <i>14th European Conference on Antennas and Propagation</i>, IEEE, 2020, doi:<a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">10.23919/eucap48036.2020.9135962</a>.","ieee":"M. Wasiak <i>et al.</i>, “Compact millimeter and submillimeter-wave photonic radiometer for cubesats,” in <i>14th European Conference on Antennas and Propagation</i>, Copenhagen, Denmark, 2020.","short":"M. Wasiak, G.S. Botello, K.A. Abdalmalak, F. Sedlmeir, A.R. Rueda Sanchez, D. Segovia-Vargas, H.G.L. Schwefel, L.E.G. Munoz, in:, 14th European Conference on Antennas and Propagation, IEEE, 2020.","ista":"Wasiak M, Botello GS, Abdalmalak KA, Sedlmeir F, Rueda Sanchez AR, Segovia-Vargas D, Schwefel HGL, Munoz LEG. 2020. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. 14th European Conference on Antennas and Propagation. EuCAP: European Conference on Antennas and Propagation.","ama":"Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave photonic radiometer for cubesats. In: <i>14th European Conference on Antennas and Propagation</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.23919/eucap48036.2020.9135962\">10.23919/eucap48036.2020.9135962</a>"},"conference":{"start_date":"2020-03-15","end_date":"2020-03-20","name":"EuCAP: European Conference on Antennas and Propagation","location":"Copenhagen, Denmark"},"publication_status":"published","type":"conference","department":[{"_id":"JoFi"}],"date_updated":"2024-03-04T10:02:49Z","language":[{"iso":"eng"}],"oa_version":"None","day":"08","_id":"15059","article_processing_charge":"No","date_published":"2020-07-08T00:00:00Z","month":"07","year":"2020","date_created":"2024-03-04T09:57:48Z","title":"Compact millimeter and submillimeter-wave photonic radiometer for cubesats"},{"month":"09","year":"2020","title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","date_created":"2024-03-04T10:03:52Z","article_type":"original","publication_status":"published","type":"journal_article","oa_version":"Published Version","author":[{"first_name":"Nikos","full_name":"Pinotsis, Nikos","last_name":"Pinotsis"},{"first_name":"Karolina","last_name":"Zielinska","full_name":"Zielinska, Karolina"},{"first_name":"Mrigya","full_name":"Babuta, Mrigya","last_name":"Babuta"},{"last_name":"Arolas","full_name":"Arolas, Joan L.","first_name":"Joan L."},{"last_name":"Kostan","full_name":"Kostan, Julius","first_name":"Julius"},{"last_name":"Khan","full_name":"Khan, Muhammad Bashir","first_name":"Muhammad Bashir"},{"last_name":"Schreiner","full_name":"Schreiner, Claudia","first_name":"Claudia"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo"},{"first_name":"Luciano","full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli"},{"first_name":"Martin","last_name":"Puchinger","full_name":"Puchinger, Martin"},{"first_name":"Eirini A.","last_name":"Gkougkoulia","full_name":"Gkougkoulia, Eirini A."},{"full_name":"Ribeiro, Euripedes de Almeida","last_name":"Ribeiro","first_name":"Euripedes de Almeida"},{"first_name":"Thomas C.","full_name":"Marlovits, Thomas C.","last_name":"Marlovits"},{"full_name":"Bhattacharya, Alok","last_name":"Bhattacharya","first_name":"Alok"},{"last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina"}],"publisher":"Proceedings of the National Academy of Sciences","abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","status":"public","volume":117,"doi":"10.1073/pnas.1917269117","quality_controlled":"1","date_published":"2020-09-08T00:00:00Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}],"language":[{"iso":"eng"}],"department":[{"_id":"CaBe"}],"date_updated":"2024-03-04T10:14:44Z","_id":"15061","day":"08","acknowledged_ssus":[{"_id":"LifeSc"}],"article_processing_charge":"No","page":"22101-22112","citation":{"mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:<a href=\"https://doi.org/10.1073/pnas.1917269117\">10.1073/pnas.1917269117</a>.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1917269117\">https://doi.org/10.1073/pnas.1917269117</a>","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1917269117\">https://doi.org/10.1073/pnas.1917269117</a>.","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(36):22101-22112. doi:<a href=\"https://doi.org/10.1073/pnas.1917269117\">10.1073/pnas.1917269117</a>","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","ieee":"N. Pinotsis <i>et al.</i>, “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       117","publication":"Proceedings of the National Academy of Sciences","issue":"36","external_id":{"pmid":["32848067"]}}]