[{"article_type":"original","department":[{"_id":"MaSe"}],"year":"2021","month":"09","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"isi":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"_id":"10067","issue":"10","publication_status":"published","external_id":{"isi":["000704414400002"],"arxiv":["2107.05735"]},"oa_version":"Preprint","type":"journal_article","publisher":"American Physical Society","author":[{"orcid":"0000-0002-5383-2869","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"full_name":"Vasseur, Romain","last_name":"Vasseur","first_name":"Romain"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"status":"public","abstract":[{"text":"The search for novel entangled phases of matter has lead to the recent discovery of a new class of “entanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r^α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.05735"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T07:24:47Z","title":"Entanglement transitions from restricted Boltzmann machines","arxiv":1,"quality_controlled":"1","date_created":"2021-10-02T09:03:42Z","citation":{"chicago":"Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement Transitions from Restricted Boltzmann Machines.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.104205\">https://doi.org/10.1103/physrevb.104.104205</a>.","apa":"Medina Ramos, R. A., Vasseur, R., &#38; Serbyn, M. (2021). Entanglement transitions from restricted Boltzmann machines. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.104205\">https://doi.org/10.1103/physrevb.104.104205</a>","mla":"Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann Machines.” <i>Physical Review B</i>, vol. 104, no. 10, 104205, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.104205\">10.1103/physrevb.104.104205</a>.","ista":"Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 104205.","ieee":"R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from restricted Boltzmann machines,” <i>Physical Review B</i>, vol. 104, no. 10. American Physical Society, 2021.","short":"R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).","ama":"Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted Boltzmann machines. <i>Physical Review B</i>. 2021;104(10). doi:<a href=\"https://doi.org/10.1103/physrevb.104.104205\">10.1103/physrevb.104.104205</a>"},"article_number":"104205","oa":1,"article_processing_charge":"No","ec_funded":1,"doi":"10.1103/physrevb.104.104205","date_published":"2021-09-30T00:00:00Z","intvolume":"       104","volume":104,"publication":"Physical Review B","acknowledgement":"We would like to thank S. De Nicola, P. Brighi, and V. Karle for fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges support from the US Department of Energy, Office of Science, Basic Energy Sciences, under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through a Sloan Research Fellowship.","day":"30"},{"publisher":"Springer Nature","publication_status":"published","external_id":{"pmid":["34584125"],"isi":["000701575500083"]},"_id":"10069","ddc":["618"],"file":[{"date_updated":"2021-10-05T14:56:48Z","content_type":"application/pdf","access_level":"open_access","date_created":"2021-10-05T14:56:48Z","file_size":6970368,"success":1,"checksum":"f002ec22f609f58e1263b79e7f79601e","file_name":"2021_ScientificReports_Robinson.pdf","relation":"main_file","creator":"cchlebak","file_id":"10091"}],"oa_version":"Published Version","type":"journal_article","year":"2021","month":"09","publication_identifier":{"eissn":["2045-2322"]},"isi":1,"article_type":"original","department":[{"_id":"MaRo"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T07:05:15Z","scopus_import":"1","abstract":[{"text":"The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups.","lang":"eng"}],"status":"public","author":[{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"first_name":"Miloš","full_name":"Stojanov, Miloš","last_name":"Stojanov"},{"first_name":"Sabine","last_name":"Blum","full_name":"Blum, Sabine"},{"first_name":"David","full_name":"Baud, David","last_name":"Baud"}],"oa":1,"article_number":"19238","quality_controlled":"1","citation":{"short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","ieee":"M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” <i>Scientific Reports</i>, vol. 11. Springer Nature, 2021.","ista":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238.","ama":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. <i>Scientific Reports</i>. 2021;11. doi:<a href=\"https://doi.org/10.1038/s41598-021-98411-z\">10.1038/s41598-021-98411-z</a>","chicago":"Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-98411-z\">https://doi.org/10.1038/s41598-021-98411-z</a>.","apa":"Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., &#38; Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-98411-z\">https://doi.org/10.1038/s41598-021-98411-z</a>","mla":"Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” <i>Scientific Reports</i>, vol. 11, 19238, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-98411-z\">10.1038/s41598-021-98411-z</a>."},"date_created":"2021-10-03T22:01:21Z","title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","pmid":1,"day":"28","publication":"Scientific Reports","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors for the computerized obstetrical data.","volume":11,"date_published":"2021-09-28T00:00:00Z","has_accepted_license":"1","intvolume":"        11","file_date_updated":"2021-10-05T14:56:48Z","doi":"10.1038/s41598-021-98411-z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes"},{"ec_funded":1,"article_processing_charge":"No","doi":"10.1016/j.jfa.2021.109234","intvolume":"       281","date_published":"2021-09-15T00:00:00Z","volume":281,"acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","day":"15","publication":"Journal of Functional Analysis","title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","date_created":"2021-10-03T22:01:21Z","citation":{"mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>, vol. 281, no. 11, 109234, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>.","apa":"Dello Schiavo, L., &#38; Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>.","ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. 2021;281(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>","short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234.","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” <i>Journal of Functional Analysis</i>, vol. 281, no. 11. Elsevier, 2021."},"arxiv":1,"quality_controlled":"1","article_number":"109234","oa":1,"author":[{"orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"},{"first_name":"Kohei","full_name":"Suzuki, Kohei","last_name":"Suzuki"}],"status":"public","abstract":[{"text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"scopus_import":"1","date_updated":"2023-08-14T07:05:44Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JaMa"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"year":"2021","month":"09","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"oa_version":"Preprint","type":"journal_article","_id":"10070","issue":"11","publication_status":"published","external_id":{"arxiv":["2008.01492"],"isi":["000703896600005"]},"publisher":"Elsevier"},{"page":"1511-1514","title":"How to tutorial-a-thon","oa":1,"quality_controlled":"1","date_created":"2021-10-03T22:01:22Z","citation":{"mla":"Adams, Henry, et al. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9, American Mathematical Society, 2021, pp. 1511–14, doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>.","chicago":"Adams, Henry, Hana Kourimska, Teresa Heiss, Sarah Percival, and Lori Ziegelmeier. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>.","apa":"Adams, H., Kourimska, H., Heiss, T., Percival, S., &#38; Ziegelmeier, L. (2021). How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>","short":"H. Adams, H. Kourimska, T. Heiss, S. Percival, L. Ziegelmeier, Notices of the American Mathematical Society 68 (2021) 1511–1514.","ieee":"H. Adams, H. Kourimska, T. Heiss, S. Percival, and L. Ziegelmeier, “How to tutorial-a-thon,” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9. American Mathematical Society, pp. 1511–1514, 2021.","ista":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. 2021. How to tutorial-a-thon. Notices of the American Mathematical Society. 68(9), 1511–1514.","ama":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. 2021;68(9):1511-1514. doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>"},"doi":"10.1090/noti2349","article_processing_charge":"No","day":"01","publication":"Notices of the American Mathematical Society","volume":68,"date_published":"2021-10-01T00:00:00Z","intvolume":"        68","month":"10","year":"2021","publication_identifier":{"eissn":["1088-9477"],"issn":["0002-9920"]},"article_type":"letter_note","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society","publication_status":"published","alternative_title":["Early Career"],"_id":"10071","issue":"9","oa_version":"Published Version","type":"journal_article","status":"public","author":[{"first_name":"Henry","last_name":"Adams","full_name":"Adams, Henry"},{"full_name":"Kourimska, Hana","last_name":"Kourimska","first_name":"Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","full_name":"Heiss, Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689"},{"first_name":"Sarah","last_name":"Percival","full_name":"Percival, Sarah"},{"last_name":"Ziegelmeier","full_name":"Ziegelmeier, Lori","first_name":"Lori"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_updated":"2021-12-03T07:31:26Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.ams.org/notices/"}]},{"oa":1,"article_number":"31","citation":{"mla":"Harris, David G., et al. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, vol. 207, 31, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>.","apa":"Harris, D. G., Iliopoulos, F., &#38; Kolmogorov, V. (2021). A new notion of commutativity for the algorithmic Lovász Local Lemma. In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i> (Vol. 207). Virtual: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","chicago":"Harris, David G., Fotis Iliopoulos, and Vladimir Kolmogorov. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Vol. 207. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>.","ama":"Harris DG, Iliopoulos F, Kolmogorov V. A new notion of commutativity for the algorithmic Lovász Local Lemma. In: <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>. Vol 207. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","ista":"Harris DG, Iliopoulos F, Kolmogorov V. 2021. A new notion of commutativity for the algorithmic Lovász Local Lemma. Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques. APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation, LIPIcs, vol. 207, 31.","short":"D.G. Harris, F. Iliopoulos, V. Kolmogorov, in:, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","ieee":"D. G. Harris, F. Iliopoulos, and V. Kolmogorov, “A new notion of commutativity for the algorithmic Lovász Local Lemma,” in <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Virtual, 2021, vol. 207."},"date_created":"2021-10-03T22:01:22Z","arxiv":1,"quality_controlled":"1","conference":{"name":"APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation","start_date":"2021-08-16","location":"Virtual","end_date":"2021-08-18"},"title":"A new notion of commutativity for the algorithmic Lovász Local Lemma","publication":"Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques","day":"15","acknowledgement":"Fotis Iliopoulos: This material is based upon work directly supported by the IAS Fund for Math and indirectly supported by the National Science Foundation Grant No. CCF-1900460. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. This work is also supported by the National Science Foundation Grant No. CCF-1815328.\r\nVladimir Kolmogorov: Supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160.","volume":207,"intvolume":"       207","has_accepted_license":"1","date_published":"2021-09-15T00:00:00Z","doi":"10.4230/LIPIcs.APPROX/RANDOM.2021.31","file_date_updated":"2021-10-06T13:51:54Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","oa_version":"Published Version","file":[{"file_name":"2021_LIPIcs_Harris.pdf","relation":"main_file","file_id":"10098","creator":"cchlebak","date_updated":"2021-10-06T13:51:54Z","access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-06T13:51:54Z","checksum":"9d2544d53aa5b01565c6891d97a4d765","success":1,"file_size":804472}],"ddc":["000"],"type":"conference","external_id":{"arxiv":["2008.05569"]},"publication_status":"published","alternative_title":["LIPIcs"],"_id":"10072","publication_identifier":{"isbn":["978-3-9597-7207-5"],"issn":["1868-8969"]},"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"month":"09","year":"2021","department":[{"_id":"VlKo"}],"date_updated":"2022-03-18T10:08:25Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The Lovász Local Lemma (LLL) is a powerful tool in probabilistic combinatorics which can be used to establish the existence of objects that satisfy certain properties. The breakthrough paper of Moser and Tardos and follow-up works revealed that the LLL has intimate connections with a class of stochastic local search algorithms for finding such desirable objects. In particular, it can be seen as a sufficient condition for this type of algorithms to converge fast. Besides conditions for existence of and fast convergence to desirable objects, one may naturally ask further questions regarding properties of these algorithms. For instance, \"are they parallelizable?\", \"how many solutions can they output?\", \"what is the expected \"weight\" of a solution?\", etc. These questions and more have been answered for a class of LLL-inspired algorithms called commutative. In this paper we introduce a new, very natural and more general notion of commutativity (essentially matrix commutativity) which allows us to show a number of new refined properties of LLL-inspired local search algorithms with significantly simpler proofs."}],"scopus_import":"1","status":"public","author":[{"first_name":"David G.","full_name":"Harris, David G.","last_name":"Harris"},{"last_name":"Iliopoulos","full_name":"Iliopoulos, Fotis","first_name":"Fotis"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” <i>Materials</i>, vol. 14, no. 18. MDPI, 2021.","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","short":"C. Chang, M. Ibáñez, Materials 14 (2021).","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. 2021;14(18). doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>, vol. 14, no. 18, 5416, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>.","chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>.","apa":"Chang, C., &#38; Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>"},"date_created":"2021-10-03T22:01:23Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"quality_controlled":"1","article_number":"5416","oa":1,"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","intvolume":"        14","has_accepted_license":"1","date_published":"2021-09-19T00:00:00Z","volume":14,"day":"19","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","publication":"Materials","pmid":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/ma14185416","file_date_updated":"2021-10-14T11:56:39Z","oa_version":"Published Version","ddc":["540"],"type":"journal_article","file":[{"date_created":"2021-10-14T11:56:39Z","checksum":"4929dfc673a3ae77c010b6174279cc1d","success":1,"file_size":4404141,"date_updated":"2021-10-14T11:56:39Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"10140","file_name":"2021_Materials_Chang.pdf"}],"issue":"18","_id":"10073","publication_status":"published","external_id":{"isi":["000700689400001"],"pmid":["34576640"]},"publisher":"MDPI","department":[{"_id":"MaIb"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["1996-1944"]},"year":"2021","month":"09","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"abstract":[{"text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-14T08:00:01Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"status":"public"},{"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","file":[{"file_name":"2021_LIPIcs_Guha.pdf","relation":"main_file","file_id":"10097","creator":"cchlebak","date_updated":"2021-10-06T12:44:05Z","access_level":"open_access","content_type":"application/pdf","date_created":"2021-10-06T12:44:05Z","file_size":825567,"checksum":"f4d407d43a97330c3fb11e6a7a6fbfb2","success":1}],"ddc":["000"],"type":"conference","oa_version":"Published Version","external_id":{"arxiv":["2105.02611"]},"alternative_title":["LIPIcs"],"publication_status":"published","_id":"10075","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-9597-7201-3"]},"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"08","year":"2021","department":[{"_id":"KrCh"}],"date_updated":"2022-05-13T08:21:56Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study the expressiveness and succinctness of good-for-games pushdown automata (GFG-PDA) over finite words, that is, pushdown automata whose nondeterminism can be resolved based on the run constructed so far, but independently of the remainder of the input word. We prove that GFG-PDA recognise more languages than deterministic PDA (DPDA) but not all context-free languages (CFL). This class is orthogonal to unambiguous CFL. We further show that GFG-PDA can be exponentially more succinct than DPDA, while PDA can be double-exponentially more succinct than GFG-PDA. We also study GFGness in visibly pushdown automata (VPA), which enjoy better closure properties than PDA, and for which we show GFGness to be ExpTime-complete. GFG-VPA can be exponentially more succinct than deterministic VPA, while VPA can be exponentially more succinct than GFG-VPA. Both of these lower bounds are tight. Finally, we study the complexity of resolving nondeterminism in GFG-PDA. Every GFG-PDA has a positional resolver, a function that resolves nondeterminism and that is only dependant on the current configuration. Pushdown transducers are sufficient to implement the resolvers of GFG-VPA, but not those of GFG-PDA. GFG-PDA with finite-state resolvers are determinisable.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","full_name":"Jecker, Ismael R"},{"last_name":"Lehtinen","full_name":"Lehtinen, Karoliina","first_name":"Karoliina"},{"last_name":"Zimmermann","full_name":"Zimmermann, Martin","first_name":"Martin"}],"oa":1,"article_number":"53","citation":{"ama":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. A bit of nondeterminism makes pushdown automata expressive and succinct. In: <i>46th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 202. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>","short":"S. Guha, I.R. Jecker, K. Lehtinen, M. Zimmermann, in:, 46th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","ieee":"S. Guha, I. R. Jecker, K. Lehtinen, and M. Zimmermann, “A bit of nondeterminism makes pushdown automata expressive and succinct,” in <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Tallinn, Estonia, 2021, vol. 202.","ista":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. 2021. A bit of nondeterminism makes pushdown automata expressive and succinct. 46th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 202, 53.","mla":"Guha, Shibashis, et al. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 202, 53, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>.","apa":"Guha, S., Jecker, I. R., Lehtinen, K., &#38; Zimmermann, M. (2021). A bit of nondeterminism makes pushdown automata expressive and succinct. In <i>46th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 202). Tallinn, Estonia: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>","chicago":"Guha, Shibashis, Ismael R Jecker, Karoliina Lehtinen, and Martin Zimmermann. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” In <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 202. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>."},"date_created":"2021-10-03T22:01:23Z","arxiv":1,"quality_controlled":"1","conference":{"location":"Tallinn, Estonia","end_date":"2021-08-27","start_date":"2021-08-23","name":"MFCS: Mathematical Foundations of Computer Science"},"title":"A bit of nondeterminism makes pushdown automata expressive and succinct","day":"18","publication":"46th International Symposium on Mathematical Foundations of Computer Science","acknowledgement":"Ismaël Jecker: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411. Karoliina Lehtinen: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 892704.","volume":202,"intvolume":"       202","has_accepted_license":"1","date_published":"2021-08-18T00:00:00Z","doi":"10.4230/LIPIcs.MFCS.2021.53","file_date_updated":"2021-10-06T12:44:05Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No"},{"volume":"12676 ","day":"17","acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","publication":"FC 2021 Workshops","date_published":"2021-09-17T00:00:00Z","doi":"10.1007/978-3-662-63958-0_34","article_processing_charge":"No","oa":1,"conference":{"name":"FC: International Conference on Financial Cryptography and Data Security","start_date":"2021-03-01","location":"Virtual","end_date":"2021-03-05"},"quality_controlled":"1","citation":{"ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: <i>FC 2021 Workshops</i>. Vol 12676. Springer Nature; 2021:431-450. doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>","ieee":"S. Blackshear <i>et al.</i>, “Reactive key-loss protection in blockchains,” in <i>FC 2021 Workshops</i>, Virtual, 2021, vol. 12676, pp. 431–450.","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: International Conference on Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450.","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In <i>FC 2021 Workshops</i> (Vol. 12676, pp. 431–450). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In <i>FC 2021 Workshops</i>, 12676:431–50. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>.","mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” <i>FC 2021 Workshops</i>, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>."},"date_created":"2021-10-03T22:01:24Z","page":"431-450","title":"Reactive key-loss protection in blockchains","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-14T07:06:16Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase   Commit()→Reveal()→Claim()−or−Challenge()  smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP)."}],"main_file_link":[{"open_access":"1","url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/"}],"author":[{"first_name":"Sam","last_name":"Blackshear","full_name":"Blackshear, Sam"},{"full_name":"Chalkias, Konstantinos","last_name":"Chalkias","first_name":"Konstantinos"},{"full_name":"Chatzigiannis, Panagiotis","last_name":"Chatzigiannis","first_name":"Panagiotis"},{"last_name":"Faizullabhoy","full_name":"Faizullabhoy, Riyaz","first_name":"Riyaz"},{"full_name":"Khaburzaniya, Irakliy","last_name":"Khaburzaniya","first_name":"Irakliy"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Joshua","full_name":"Lind, Joshua","last_name":"Lind"},{"first_name":"David","full_name":"Wong, David","last_name":"Wong"},{"first_name":"Tim","full_name":"Zakian, Tim","last_name":"Zakian"}],"status":"public","publisher":"Springer Nature","_id":"10076","alternative_title":["LNCS"],"external_id":{"isi":["000713005000034"]},"publication_status":"published","type":"conference","oa_version":"Preprint","month":"09","year":"2021","isi":1,"publication_identifier":{"eisbn":["978-3-662-63958-0"],"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-6626-3957-3"]},"department":[{"_id":"ElKo"}]},{"author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"},{"full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"}],"ec_funded":1,"article_processing_charge":"No","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"doi":"10.1101/2021.09.28.460602","date_published":"2021-09-29T00:00:00Z","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"}]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-25T23:30:09Z","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","day":"29","publication":"bioRxiv","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"month":"09","year":"2021","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"_id":"10077","publication_status":"submitted","date_created":"2021-10-04T06:23:34Z","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>."},"type":"preprint","oa_version":"Preprint","oa":1,"publisher":"Cold Spring Harbor Laboratory"},{"date_published":"2021-10-02T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.30.462269","open_access":"1"}],"abstract":[{"lang":"eng","text":"Hippocampal and neocortical neural activity is modulated by the position of the individual in space. While hippocampal neurons provide the basis for a spatial map, prefrontal cortical neurons generalize over environmental features. Whether these generalized representations result from a bidirectional interaction with, or are mainly derived from hippocampal spatial representations is not known. By examining simultaneously recorded hippocampal and medial prefrontal neurons, we observed that prefrontal spatial representations show a delayed coherence with hippocampal ones. We also identified subpopulations of cells in the hippocampus and medial prefrontal cortex that formed functional cross-area couplings; these resembled the optimal connections predicted by a probabilistic model of spatial information transfer and generalization. Moreover, cross-area couplings were strongest and had the shortest delay preceding spatial decision-making. Our results suggest that generalized spatial coding in the medial prefrontal cortex is inherited from spatial representations in the hippocampus, and that the routing of information can change dynamically with behavioral demands."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"day":"02","publication":"bioRxiv","acknowledgement":"We thank Federico Stella for invaluable suggestions and discussions. We thank Yosman BapatDhar and Andrea Cumpelik for comments, help and suggestions on the exposure of the text. We thank Predrag Živadinović and Juliana Couras for comments on the text and the figures. This work was supported by the EU-FP7 MC-ITN IN-SENS (grant 607616).","date_updated":"2021-10-05T12:34:26Z","status":"public","author":[{"first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","last_name":"Nardin","full_name":"Nardin, Michele"},{"first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","last_name":"Käfer"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"ec_funded":1,"article_processing_charge":"No","doi":"10.1101/2021.09.30.462269","publication_status":"submitted","_id":"10080","oa_version":"Preprint","type":"preprint","citation":{"mla":"Nardin, Michele, et al. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","apa":"Nardin, M., Käfer, K., &#38; Csicsvari, J. L. (n.d.). The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>","chicago":"Nardin, Michele, Karola Käfer, and Jozsef L Csicsvari. “The Generalized Spatial Representation in the Prefrontal Cortex Is Inherited from the Hippocampus.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.30.462269\">https://doi.org/10.1101/2021.09.30.462269</a>.","ama":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>","ieee":"M. Nardin, K. Käfer, and J. L. Csicsvari, “The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Nardin M, Käfer K, Csicsvari JL. The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.30.462269\">10.1101/2021.09.30.462269</a>.","short":"M. Nardin, K. Käfer, J.L. Csicsvari, BioRxiv (n.d.)."},"date_created":"2021-10-04T06:28:32Z","oa":1,"publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"title":"The generalized spatial representation in the prefrontal cortex is inherited from the hippocampus","project":[{"grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia"}],"month":"10","year":"2021"},{"oa":1,"citation":{"short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>.","apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>"},"date_created":"2021-10-04T13:33:10Z","title":"Rapid cell growth regulation in Arabidopsis","day":"06","date_published":"2021-10-06T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","file_date_updated":"2022-12-20T23:30:03Z","doi":"10.15479/at:ista:10083","article_processing_charge":"No","ec_funded":1,"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"supervisor":[{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","_id":"10083","alternative_title":["ISTA Thesis"],"publication_status":"published","file":[{"file_size":8616142,"checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","date_created":"2021-10-14T08:00:07Z","embargo":"2022-10-14","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-12-20T23:30:03Z","file_id":"10138","creator":"cchlebak","relation":"main_file","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf"},{"relation":"source_file","file_id":"10139","creator":"cchlebak","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","embargo_to":"open_access","date_created":"2021-10-14T08:00:13Z","file_size":15058499,"checksum":"f23ed258ca894f6aabf58b0c128bf242","date_updated":"2022-12-20T23:30:03Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"type":"dissertation","ddc":["575"],"oa_version":"Published Version","month":"10","year":"2021","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-05-07T11:12:33Z","abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"related_material":{"record":[{"id":"442","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8931"},{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8283"},{"status":"public","relation":"part_of_dissertation","id":"8986"},{"relation":"part_of_dissertation","status":"public","id":"10015"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"relation":"part_of_dissertation","status":"public","id":"6627"}]},"author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"status":"public"},{"oa_version":"Preprint","type":"preprint","_id":"10095","publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"year":"2021","month":"09","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_updated":"2024-10-29T10:22:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"},{"id":"10223","relation":"later_version","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"author":[{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li"},{"orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"first_name":"Wouter","full_name":"Smet, Wouter","last_name":"Smet"},{"first_name":"Hong","full_name":"Ren, Hong","last_name":"Ren"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Sergey","full_name":"Shabala, Sergey","last_name":"Shabala"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","article_number":"266395","oa":1,"date_created":"2021-10-06T08:56:22Z","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395."},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","publication":"Research Square","day":"09","date_published":"2021-09-09T00:00:00Z","doi":"10.21203/rs.3.rs-266395/v3","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"doi":"10.3390/v13091853","file_date_updated":"2021-10-08T10:38:15Z","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13,"day":"17","publication":"Viruses","acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","pmid":1,"intvolume":"        13","has_accepted_license":"1","date_published":"2021-09-17T00:00:00Z","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","article_number":"1853","oa":1,"citation":{"apa":"Obr, M., Schur, F. K., &#38; Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. MDPI. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>","chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>.","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>, vol. 13, no. 9, 1853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>.","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. 2021;13(9). doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” <i>Viruses</i>, vol. 13, no. 9. MDPI, 2021.","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021)."},"date_created":"2021-10-07T09:13:29Z","quality_controlled":"1","author":[{"orcid":"0000-0003-1756-6564","full_name":"Obr, Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."}],"status":"public","date_updated":"2023-08-14T07:21:51Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.","lang":"eng"}],"keyword":["virology","infectious diseases"],"isi":1,"publication_identifier":{"issn":["1999-4915"]},"year":"2021","month":"09","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"FlSc"}],"article_type":"original","publisher":"MDPI","file":[{"file_name":"2021_Viruses_Obr.pdf","creator":"cchlebak","file_id":"10115","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-10-08T10:38:15Z","file_size":4146796,"checksum":"bcfd72a12977d48e22df3d0cc55aacf1","success":1,"date_created":"2021-10-08T10:38:15Z"}],"ddc":["616"],"oa_version":"Published Version","type":"journal_article","issue":"9","_id":"10103","publication_status":"published","external_id":{"isi":["000699841100001"],"pmid":["34578434"]}},{"date_created":"2021-10-07T23:30:10Z","citation":{"apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). Differential monitoring. In <i>International Conference on Runtime Verification</i> (Vol. 12974, pp. 231–243). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In <i>International Conference on Runtime Verification</i>, 12974:231–43. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” <i>International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: <i>International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in <i>International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 231–243.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243."},"conference":{"end_date":"2021-10-14","location":"Virtual","start_date":"2021-10-11","name":"RV: Runtime Verification"},"quality_controlled":"1","oa":1,"title":"Differential monitoring","page":"231-243","has_accepted_license":"1","intvolume":"     12974","date_published":"2021-10-06T00:00:00Z","volume":12974,"publication":"International Conference on Runtime Verification","day":"06","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","place":"Cham","article_processing_charge":"No","doi":"10.1007/978-3-030-88494-9_12","file_date_updated":"2021-10-07T23:32:18Z","oa_version":"Preprint","file":[{"creator":"fmuehlbo","file_id":"10109","relation":"main_file","file_name":"differentialmonitoring-cameraready-openaccess.pdf","checksum":"554c7fdb259eda703a8b6328a6dad55a","file_size":350632,"success":1,"date_created":"2021-10-07T23:32:18Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-10-07T23:32:18Z"}],"ddc":["005"],"type":"conference","_id":"10108","publication_status":"published","external_id":{"isi":["000719383800012"]},"alternative_title":["LNCS"],"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"isi":1,"publication_identifier":{"isbn":["978-3-030-88493-2"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-030-88494-9"]},"year":"2021","month":"10","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"keyword":["run-time verification","software engineering","implicit specification"],"related_material":{"record":[{"id":"9946","status":"public","relation":"extended_version"}]},"scopus_import":"1","date_updated":"2023-08-14T07:20:30Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"author":[{"full_name":"Mühlböck, Fabian","last_name":"Mühlböck","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"status":"public"},{"abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/spot-the-difference/","relation":"press_release","description":"News on IST Webpage"}],"record":[{"id":"10816","status":"public","relation":"used_for_analysis_in"}]},"has_accepted_license":"1","date_published":"2021-12-16T00:00:00Z","date_updated":"2024-03-25T23:30:07Z","day":"16","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Guzmán, José","last_name":"Guzmán","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100"},{"orcid":"0000-0003-4710-2082","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"}],"tmp":{"name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","short":"GPL 3.0"},"status":"public","doi":"10.15479/AT:ISTA:10110","license":"https://opensource.org/licenses/GPL-3.0","file_date_updated":"2021-10-08T08:46:04Z","date_created":"2021-10-08T06:44:22Z","citation":{"short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>"},"ddc":["005"],"type":"software","file":[{"creator":"cchlebak","file_id":"10114","relation":"main_file","file_name":"patternseparation-main (1).zip","file_size":332990101,"success":1,"checksum":"f92f8931cad0aa7e411c1715337bf408","date_created":"2021-10-08T08:46:04Z","content_type":"application/x-zip-compressed","access_level":"open_access","date_updated":"2021-10-08T08:46:04Z"}],"_id":"10110","publisher":"IST Austria","oa":1,"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"year":"2021","month":"12"},{"date_published":"2021-09-17T00:00:00Z","has_accepted_license":"1","intvolume":"        10","pmid":1,"acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","publication":"eLife","day":"17","volume":10,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","file_date_updated":"2021-10-11T14:15:07Z","doi":"10.7554/eLife.68238","quality_controlled":"1","date_created":"2021-10-10T22:01:22Z","citation":{"apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., &#38; de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>.","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>, vol. 10, e68238, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>.","ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"oa":1,"article_number":"e68238","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","scopus_import":"1","abstract":[{"text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-14T07:23:39Z","status":"public","author":[{"full_name":"Vuong-Brender, Thanh","last_name":"Vuong-Brender","first_name":"Thanh","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E"},{"first_name":"Sean","last_name":"Flynn","full_name":"Flynn, Sean"},{"id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","first_name":"Yvonne","last_name":"Vallis","full_name":"Vallis, Yvonne"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"De Bono","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443"}],"external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"publication_status":"published","_id":"10116","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2021-10-11T14:15:07Z","success":1,"checksum":"b465e172d2b1f57aa26a2571a085d052","file_size":1774624,"date_created":"2021-10-11T14:15:07Z","file_name":"2021_eLife_VuongBrender.pdf","file_id":"10122","creator":"cchlebak","relation":"main_file"}],"ddc":["610"],"publisher":"eLife Sciences Publications","article_type":"original","department":[{"_id":"MaDe"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"year":"2021","month":"09","publication_identifier":{"eissn":["2050-084X"]},"isi":1},{"date_created":"2021-10-10T22:01:23Z","citation":{"short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>.","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>."},"quality_controlled":"1","oa":1,"article_number":"101094","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","intvolume":"       297","has_accepted_license":"1","date_published":"2021-09-01T00:00:00Z","publication":"Journal of Biological Chemistry","day":"01","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","volume":297,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"Yes","doi":"10.1016/J.JBC.2021.101094","file_date_updated":"2021-10-11T12:20:58Z","type":"journal_article","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2021-10-11T12:20:58Z","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","success":1,"file_size":1680010,"date_created":"2021-10-11T12:20:58Z","file_name":"2021_JBC_Artan.pdf","creator":"cchlebak","file_id":"10121","relation":"main_file"}],"ddc":["612"],"oa_version":"Published Version","external_id":{"isi":["000706409200006"]},"publication_status":"published","issue":"3","_id":"10117","publisher":"Elsevier","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"article_type":"original","publication_identifier":{"issn":["0021-9258"],"eissn":["1083-351X"]},"isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"month":"09","year":"2021","abstract":[{"text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-14T07:24:09Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"full_name":"Barratt, Stephen","last_name":"Barratt","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen"},{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"first_name":"Farida","last_name":"Begum","full_name":"Begum, Farida"},{"last_name":"Skehel","full_name":"Skehel, Mark","first_name":"Mark"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","full_name":"Nicolas, Armel","last_name":"Nicolas"},{"last_name":"De Bono","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}]},{"doi":"10.1002/adma.202106858","file_date_updated":"2022-02-03T13:16:14Z","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":33,"day":"29","acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","publication":"Advanced Materials","pmid":1,"has_accepted_license":"1","intvolume":"        33","date_published":"2021-12-29T00:00:00Z","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","article_number":"2106858","oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_created":"2021-10-11T20:07:24Z","citation":{"mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>, vol. 33, no. 52, 2106858, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>.","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>","ieee":"Y. Liu <i>et al.</i>, “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” <i>Advanced Materials</i>, vol. 33, no. 52. Wiley, 2021.","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. 2021;33(52). doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>"},"quality_controlled":"1","author":[{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcabrini, Mariano","last_name":"Calcabrini","orcid":"0000-0003-4566-5877","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yu, Yuan","last_name":"Yu","first_name":"Yuan"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"full_name":"Chang, Cheng","last_name":"Chang","orcid":"0000-0002-9515-4277","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"first_name":"Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815"},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"first_name":"Oana","last_name":"Cojocaru‐Mirédin","full_name":"Cojocaru‐Mirédin, Oana"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria"}],"status":"public","date_updated":"2023-08-14T07:25:27Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials.","lang":"eng"}],"related_material":{"record":[{"id":"12885","status":"public","relation":"dissertation_contains"}]},"keyword":["mechanical engineering","mechanics of materials","general materials science"],"scopus_import":"1","isi":1,"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"month":"12","year":"2021","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"article_type":"original","publisher":"Wiley","oa_version":"Published Version","file":[{"date_created":"2022-02-03T13:16:14Z","checksum":"990bccc527c64d85cf1c97885110b5f4","file_size":5595666,"success":1,"date_updated":"2022-02-03T13:16:14Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","file_id":"10720","file_name":"2021_AdvancedMaterials_Liu.pdf"}],"ddc":["620"],"type":"journal_article","issue":"52","_id":"10123","publication_status":"published","external_id":{"isi":["000709899300001"],"pmid":["34626034"]}},{"author":[{"first_name":"Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","orcid":"0000-0003-4982-5970","last_name":"Suzuki","full_name":"Suzuki, Fumika"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Zurek","full_name":"Zurek, Wojciech H.","first_name":"Wojciech H."},{"last_name":"Krems","full_name":"Krems, Roman V.","first_name":"Roman V."}],"status":"public","date_updated":"2024-02-29T12:34:10Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics.","lang":"eng"}],"keyword":["General Physics and Astronomy"],"main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"scopus_import":"1","isi":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"10","year":"2021","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"MiLe"}],"article_type":"original","publisher":"American Physical Society ","oa_version":"Preprint","type":"journal_article","_id":"10134","issue":"16","external_id":{"arxiv":["2011.06279"],"isi":["000707495700001"]},"publication_status":"published","doi":"10.1103/physrevlett.127.160602","article_processing_charge":"No","ec_funded":1,"volume":127,"publication":"Physical Review Letters","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","day":"12","intvolume":"       127","date_published":"2021-10-12T00:00:00Z","title":"Anderson localization of composite particles","article_number":"160602","oa":1,"date_created":"2021-10-13T09:21:33Z","citation":{"chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>. American Physical Society , 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>.","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., &#38; Krems, R. V. (2021). Anderson localization of composite particles. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>","mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>.","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” <i>Physical Review Letters</i>, vol. 127, no. 16. American Physical Society , 2021.","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. <i>Physical Review Letters</i>. 2021;127(16). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>"},"arxiv":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-01-25T10:53:29Z","related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects."}],"status":"public","author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","last_name":"Semerádová","full_name":"Semerádová, Hana"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"10135","ddc":["570"],"oa_version":"Published Version","type":"dissertation","file":[{"file_size":28508629,"checksum":"ce7108853e6cec6224f17cd6429b51fe","embargo_to":"open_access","date_created":"2021-10-27T07:45:37Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-12-20T23:30:05Z","file_id":"10186","creator":"cziletti","relation":"source_file","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx"},{"relation":"main_file","file_id":"10187","creator":"cziletti","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","date_created":"2021-10-27T07:45:57Z","file_size":10623525,"checksum":"0d7afb846e8e31ec794de47bf44e12ef","date_updated":"2022-12-20T23:30:05Z","access_level":"open_access","embargo":"2022-10-28","content_type":"application/pdf"}],"project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746"}],"month":"10","year":"2021","publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"day":"13","date_published":"2021-10-13T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","file_date_updated":"2022-12-20T23:30:05Z","doi":"10.15479/at:ista:10135","article_processing_charge":"No","oa":1,"date_created":"2021-10-13T13:42:48Z","citation":{"ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","mla":"Semerádová, Hana. <i>Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10135\">10.15479/at:ista:10135</a>.","apa":"Semerádová, H. (2021). <i>Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>","chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10135\">https://doi.org/10.15479/at:ista:10135</a>."},"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis"}]