[{"main_file_link":[{"url":"https://doi.org/10.1002/chem.202200807","open_access":"1"}],"scopus_import":"1","citation":{"mla":"Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” Chemistry - A European Journal, vol. 28, no. 30, e202200807, Wiley, 2022, doi:10.1002/chem.202200807.","ista":"Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M, Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.","apa":"Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa, K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.202200807","chicago":"Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim, Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” Chemistry - A European Journal. Wiley, 2022. https://doi.org/10.1002/chem.202200807.","short":"S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J. Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).","ama":"Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. 2022;28(30). doi:10.1002/chem.202200807","ieee":"S. Thayyil et al., “Dynamic control of microbial movement by photoswitchable ATP antagonists,” Chemistry - A European Journal, vol. 28, no. 30. Wiley, 2022."},"intvolume":" 28","publication_status":"published","doi":"10.1002/chem.202200807","oa_version":"Published Version","date_published":"2022-05-25T00:00:00Z","status":"public","publication_identifier":{"eissn":["15213765"],"issn":["09476539"]},"oa":1,"month":"05","date_updated":"2023-10-03T10:58:31Z","issue":"30","abstract":[{"text":"Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.","lang":"eng"}],"year":"2022","article_number":"e202200807","_id":"11333","article_processing_charge":"No","article_type":"original","external_id":{"isi":["000781658800001"],"pmid":["35332959"]},"volume":28,"quality_controlled":"1","date_created":"2022-04-24T22:01:44Z","publication":"Chemistry - A European Journal","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dynamic control of microbial movement by photoswitchable ATP antagonists","pmid":1,"day":"25","isi":1,"author":[{"full_name":"Thayyil, Sampreeth","first_name":"Sampreeth","last_name":"Thayyil"},{"first_name":"Yukinori","last_name":"Nishigami","full_name":"Nishigami, Yukinori"},{"full_name":"Islam, Muhammad J","id":"C94881D2-008F-11EA-8E08-2637E6697425","last_name":"Islam","first_name":"Muhammad J"},{"full_name":"Hashim, P. K.","first_name":"P. K.","last_name":"Hashim"},{"full_name":"Furuta, Ken'Ya","first_name":"Ken'Ya","last_name":"Furuta"},{"full_name":"Oiwa, Kazuhiro","first_name":"Kazuhiro","last_name":"Oiwa"},{"full_name":"Yu, Jian","last_name":"Yu","first_name":"Jian"},{"full_name":"Yao, Min","first_name":"Min","last_name":"Yao"},{"last_name":"Nakagaki","first_name":"Toshiyuki","full_name":"Nakagaki, Toshiyuki"},{"full_name":"Tamaoki, Nobuyuki","first_name":"Nobuyuki","last_name":"Tamaoki"}]},{"article_processing_charge":"No","article_type":"original","volume":76,"quality_controlled":"1","external_id":{"isi":["000781632500001"],"pmid":["35323995"]},"publication":"Evolution","date_created":"2022-04-24T22:01:44Z","page":"899-914","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"01","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"pmid":1,"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","file":[{"relation":"main_file","content_type":"application/pdf","file_size":2855214,"success":1,"date_updated":"2022-08-05T06:19:28Z","file_name":"2022_Evolution_Freitas.pdf","date_created":"2022-08-05T06:19:28Z","checksum":"c27c025ae9afcf6c804d46a909775ee5","file_id":"11729","creator":"dernst","access_level":"open_access"}],"author":[{"full_name":"Freitas, Susana","last_name":"Freitas","first_name":"Susana"},{"full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Schwander","first_name":"Tanja","full_name":"Schwander, Tanja"},{"last_name":"Arakelyan","first_name":"Marine","full_name":"Arakelyan, Marine"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"full_name":"Kumlutas, Yusuf","first_name":"Yusuf","last_name":"Kumlutas"},{"full_name":"Harris, David James","first_name":"David James","last_name":"Harris"},{"full_name":"Carretero, Miguel A.","last_name":"Carretero","first_name":"Miguel A."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"isi":1,"project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"ddc":["570"],"scopus_import":"1","file_date_updated":"2022-08-05T06:19:28Z","citation":{"chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. Wiley. https://doi.org/10.1111/evo.14462","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","ieee":"S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” Evolution, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462"},"intvolume":" 76","doi":"10.1111/evo.14462","publication_status":"published","date_published":"2022-05-01T00:00:00Z","oa_version":"Published Version","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"oa":1,"status":"public","ec_funded":1,"month":"05","year":"2022","abstract":[{"text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.","lang":"eng"}],"issue":"5","date_updated":"2023-08-03T07:00:28Z","_id":"11334"},{"article_type":"original","article_processing_charge":"No","related_material":{"link":[{"url":"https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/","relation":"press_release","description":"News on ISTA website"}]},"volume":8,"quality_controlled":"1","date_created":"2022-04-26T15:04:50Z","publication":"Science Advances","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"type":"journal_article","title":"Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression","publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit) and S. Gharagozlou for technical support. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Lab Support Facility (LSF), and Preclinical Facility (PCF). N.A. received funding from the FWF Firnberg-Programm (T 1031). The work was supported by IST institutional funds and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","file":[{"relation":"main_file","content_type":"application/pdf","file_size":2973998,"success":1,"creator":"patrickd","file_id":"12742","checksum":"0117023e188542082ca6693cf39e7f03","access_level":"open_access","file_name":"sciadv.abq1263.pdf","date_updated":"2023-03-21T14:18:10Z","date_created":"2023-03-21T14:18:10Z"}],"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"}],"author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole"},{"full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"file_date_updated":"2023-03-21T14:18:10Z","scopus_import":"1","intvolume":" 8","citation":{"ama":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. Science Advances. 2022;8(44). doi:10.1126/sciadv.abq1263","ieee":"N. Amberg, F. Pauler, C. Streicher, and S. Hippenmeyer, “Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression,” Science Advances, vol. 8, no. 44. American Association for the Advancement of Science, 2022.","short":"N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).","apa":"Amberg, N., Pauler, F., Streicher, C., & Hippenmeyer, S. (2022). Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abq1263","ista":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. 2022. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. Science Advances. 8(44), abq1263.","mla":"Amberg, Nicole, et al. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” Science Advances, vol. 8, no. 44, abq1263, American Association for the Advancement of Science, 2022, doi:10.1126/sciadv.abq1263.","chicago":"Amberg, Nicole, Florian Pauler, Carmen Streicher, and Simon Hippenmeyer. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” Science Advances. American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.abq1263."},"publication_status":"published","doi":"10.1126/sciadv.abq1263","date_published":"2022-11-01T00:00:00Z","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["2375-2548"]},"status":"public","ec_funded":1,"month":"11","year":"2022","date_updated":"2023-05-31T12:24:10Z","abstract":[{"lang":"eng","text":"The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior."}],"issue":"44","_id":"11336","article_number":"abq1263","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}]},{"publication_identifier":{"issn":["2469-9950"],"eisbn":["2469-9969"]},"oa":1,"status":"public","ec_funded":1,"month":"04","year":"2022","arxiv":1,"abstract":[{"text":"Nonanalytic points in the return probability of a quantum state as a function of time, known as dynamical quantum phase transitions (DQPTs), have received great attention in recent years, but the understanding of their mechanism is still incomplete. In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical precession and entanglement generation, leading to the definition of precession (pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional systems by considering semi-infinite ladders of varying width. For square lattices, we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement gap, while eDQPTs correspond to suppressed local observables and avoided crossings in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder width and other details, challenging the extrapolation to the thermodynamic limit especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that lattices with an odd number of nearest neighbors give rise to phenomenologies beyond the one-dimensional classification.","lang":"eng"}],"date_updated":"2023-08-03T06:33:33Z","_id":"11337","article_number":"165149","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2112.11273"}],"citation":{"apa":"De Nicola, S., Michailidis, A., & Serbyn, M. (2022). Entanglement and precession in two-dimensional dynamical quantum phase transitions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.105.165149","mla":"De Nicola, Stefano, et al. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” Physical Review B, vol. 105, 165149, American Physical Society, 2022, doi:10.1103/PhysRevB.105.165149.","ista":"De Nicola S, Michailidis A, Serbyn M. 2022. Entanglement and precession in two-dimensional dynamical quantum phase transitions. Physical Review B. 105, 165149.","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.105.165149.","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement and precession in two-dimensional dynamical quantum phase transitions,” Physical Review B, vol. 105. American Physical Society, 2022.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement and precession in two-dimensional dynamical quantum phase transitions. Physical Review B. 2022;105. doi:10.1103/PhysRevB.105.165149","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022)."},"intvolume":" 105","doi":"10.1103/PhysRevB.105.165149","publication_status":"published","date_published":"2022-04-15T00:00:00Z","oa_version":"Preprint","title":"Entanglement and precession in two-dimensional dynamical quantum phase transitions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","day":"15","acknowledgement":"We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).\r\nS.D.N. also acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","isi":1,"author":[{"first_name":"Stefano","orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","full_name":"De Nicola, Stefano"},{"first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"article_type":"original","article_processing_charge":"No","volume":105,"quality_controlled":"1","external_id":{"arxiv":["2112.11273"],"isi":["000806812400004"]},"publication":"Physical Review B","date_created":"2022-04-28T08:06:10Z","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Communications Biology","date_created":"2022-05-01T22:01:41Z","has_accepted_license":"1","volume":5,"quality_controlled":"1","external_id":{"isi":["000784143400001"],"pmid":["35444215"]},"article_type":"original","article_processing_charge":"No","file":[{"access_level":"open_access","file_id":"11342","creator":"dernst","checksum":"7c6f76ab17393d650825cc240edc84b3","date_created":"2022-05-02T06:26:26Z","date_updated":"2022-05-02T06:26:26Z","file_name":"2022_CommBiology_Glover.pdf","file_size":2827723,"success":1,"content_type":"application/pdf","relation":"main_file"}],"isi":1,"author":[{"first_name":"Georgina","last_name":"Glover","full_name":"Glover, Georgina"},{"full_name":"Voliotis, Margaritis","first_name":"Margaritis","last_name":"Voliotis"},{"full_name":"Łapińska, Urszula","last_name":"Łapińska","first_name":"Urszula"},{"full_name":"Invergo, Brandon M.","first_name":"Brandon M.","last_name":"Invergo"},{"full_name":"Soanes, Darren","first_name":"Darren","last_name":"Soanes"},{"first_name":"Paul","last_name":"O’Neill","full_name":"O’Neill, Paul"},{"first_name":"Karen","last_name":"Moore","full_name":"Moore, Karen"},{"first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","full_name":"Nikolic, Nela"},{"first_name":"Peter","last_name":"Petrov","full_name":"Petrov, Peter"},{"first_name":"David S.","last_name":"Milner","full_name":"Milner, David S."},{"first_name":"Sumita","last_name":"Roy","full_name":"Roy, Sumita"},{"first_name":"Kate","last_name":"Heesom","full_name":"Heesom, Kate"},{"full_name":"Richards, Thomas A.","last_name":"Richards","first_name":"Thomas A."},{"full_name":"Tsaneva-Atanasova, Krasimira","first_name":"Krasimira","last_name":"Tsaneva-Atanasova"},{"last_name":"Pagliara","first_name":"Stefano","full_name":"Pagliara, Stefano"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"20","acknowledgement":"G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1). M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1). U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I. acknowledges support from a Wellcome Trust Institutional Strategic Support Award to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).","pmid":1,"title":"Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","date_published":"2022-04-20T00:00:00Z","oa_version":"Published Version","doi":"10.1038/s42003-022-03336-6","publication_status":"published","intvolume":" 5","citation":{"mla":"Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” Communications Biology, vol. 5, 385, Springer Nature, 2022, doi:10.1038/s42003-022-03336-6.","ista":"Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.","apa":"Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill, P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03336-6","chicago":"Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03336-6.","ama":"Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. 2022;5. doi:10.1038/s42003-022-03336-6","ieee":"G. Glover et al., “Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells,” Communications Biology, vol. 5. Springer Nature, 2022.","short":"G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill, K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards, K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022)."},"ddc":["570"],"scopus_import":"1","file_date_updated":"2022-05-02T06:26:26Z","_id":"11339","article_number":"385","year":"2022","abstract":[{"text":"The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.","lang":"eng"}],"date_updated":"2023-08-03T06:45:26Z","month":"04","publication_identifier":{"eissn":["2399-3642"]},"oa":1,"status":"public"},{"_id":"11340","date_updated":"2023-08-03T06:42:50Z","arxiv":1,"issue":"16","abstract":[{"text":"Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.","lang":"eng"}],"year":"2022","month":"04","status":"public","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"oa":1,"oa_version":"Preprint","date_published":"2022-04-14T00:00:00Z","publication_status":"published","doi":"10.1021/acs.jpcb.2c00028","citation":{"chicago":"Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” Journal of Physical Chemistry B. American Chemical Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.","mla":"Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” Journal of Physical Chemistry B, vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.","apa":"Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., & Trizac, E. (2022). Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028","ista":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. 126(16), 3143–3149.","short":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical Chemistry B 126 (2022) 3143–3149.","ieee":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring,” Journal of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp. 3143–3149, 2022.","ama":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028"},"intvolume":" 126","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2203.10524","open_access":"1"}],"isi":1,"author":[{"orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan"},{"first_name":"Abhay","last_name":"Goyal","full_name":"Goyal, Abhay"},{"first_name":"Emanuela","last_name":"Del Gado","full_name":"Del Gado, Emanuela"},{"last_name":"Šamaj","first_name":"Ladislav","full_name":"Šamaj, Ladislav"},{"full_name":"Trizac, Emmanuel","first_name":"Emmanuel","last_name":"Trizac"}],"acknowledgement":"We thank Martin Trulsson for useful discussions and for providing us with simulation data. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21 is acknowledged.","day":"14","publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"page":"3143-3149","date_created":"2022-05-01T22:01:42Z","publication":"Journal of Physical Chemistry B","external_id":{"isi":["000796953700022"],"arxiv":["2203.10524"]},"quality_controlled":"1","volume":126,"article_processing_charge":"No","article_type":"original"},{"has_accepted_license":"1","publication":"Nonlinear Dynamics","page":"3209-3218","date_created":"2022-05-02T07:01:59Z","type":"journal_article","department":[{"_id":"KiMo"}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","keyword":["Electrical and Electronic Engineering","Applied Mathematics","Mechanical Engineering","Ocean Engineering","Aerospace Engineering","Control and Systems Engineering"],"volume":108,"quality_controlled":"1","external_id":{"isi":["000784871800001"]},"acknowledgement":"The authors thank Enrique Calisto,Michal Kowalczyk, and Michel Ferre for fructified discussions. This work was funded by ANID—Millennium Science Initiative Program—ICN17_012. MGC is thankful for financial support from the Fondecyt 1210353 project.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"author":[{"full_name":"Aguilera, Esteban","last_name":"Aguilera","first_name":"Esteban"},{"full_name":"Clerc, Marcel G.","last_name":"Clerc","first_name":"Marcel G."},{"first_name":"Valeska","last_name":"Zambra","id":"467ed36b-dc96-11ea-b7c8-b043a380b282","full_name":"Zambra, Valeska"}],"file":[{"checksum":"7d80cdece4e1b1c2106e6772a9622f60","file_id":"11728","creator":"dernst","access_level":"open_access","file_name":"2022_NonlinearDyn_Aguilera.pdf","date_updated":"2022-08-05T06:13:19Z","date_created":"2022-08-05T06:13:19Z","relation":"main_file","content_type":"application/pdf","file_size":1416049,"success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Vortices nucleation by inherent fluctuations in nematic liquid crystal cells","doi":"10.1007/s11071-022-07396-5","publication_status":"published","oa_version":"Published Version","date_published":"2022-06-01T00:00:00Z","file_date_updated":"2022-08-05T06:13:19Z","scopus_import":"1","ddc":["530"],"citation":{"ista":"Aguilera E, Clerc MG, Zambra V. 2022. Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics. 108, 3209–3218.","mla":"Aguilera, Esteban, et al. “Vortices Nucleation by Inherent Fluctuations in Nematic Liquid Crystal Cells.” Nonlinear Dynamics, vol. 108, Springer Nature, 2022, pp. 3209–18, doi:10.1007/s11071-022-07396-5.","apa":"Aguilera, E., Clerc, M. G., & Zambra, V. (2022). Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics. Springer Nature. https://doi.org/10.1007/s11071-022-07396-5","chicago":"Aguilera, Esteban, Marcel G. Clerc, and Valeska Zambra. “Vortices Nucleation by Inherent Fluctuations in Nematic Liquid Crystal Cells.” Nonlinear Dynamics. Springer Nature, 2022. https://doi.org/10.1007/s11071-022-07396-5.","short":"E. Aguilera, M.G. Clerc, V. Zambra, Nonlinear Dynamics 108 (2022) 3209–3218.","ama":"Aguilera E, Clerc MG, Zambra V. Vortices nucleation by inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics. 2022;108:3209-3218. doi:10.1007/s11071-022-07396-5","ieee":"E. Aguilera, M. G. Clerc, and V. Zambra, “Vortices nucleation by inherent fluctuations in nematic liquid crystal cells,” Nonlinear Dynamics, vol. 108. Springer Nature, pp. 3209–3218, 2022."},"intvolume":" 108","abstract":[{"text":"Multistable systems are characterized by exhibiting domain coexistence, where each domain accounts for the different equilibrium states. In case these systems are described by vectorial fields, domains can be connected through topological defects. Vortices are one of the most frequent and studied topological defect points. Optical vortices are equally relevant for their fundamental features as beams with topological features and their applications in image processing, telecommunications, optical tweezers, and quantum information. A natural source of optical vortices is the interaction of light beams with matter vortices in liquid crystal cells. The rhythms that govern the emergence of matter vortices due to fluctuations are not established. Here, we investigate the nucleation mechanisms of the matter vortices in liquid crystal cells and establish statistical laws that govern them. Based on a stochastic amplitude equation, the law for the number of nucleated vortices as a function of anisotropy, voltage, and noise level intensity is set. Experimental observations in a nematic liquid crystal cell with homeotropic anchoring and a negative anisotropic dielectric constant under the influence of a transversal electric field show a qualitative agreement with the theoretical findings.","lang":"eng"}],"date_updated":"2023-08-03T06:46:54Z","year":"2022","_id":"11343","status":"public","publication_identifier":{"issn":["0924-090X"],"eissn":["1573-269X"]},"oa":1,"month":"06"},{"doi":"10.1038/s41598-022-10827-3","publication_status":"published","date_published":"2022-04-27T00:00:00Z","oa_version":"Published Version","ddc":["570"],"scopus_import":"1","file_date_updated":"2022-05-02T09:05:20Z","intvolume":" 12","citation":{"short":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022).","ama":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 2022;12. doi:10.1038/s41598-022-10827-3","ieee":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific Reports, vol. 12. Springer Nature, 2022.","chicago":"Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3.","apa":"Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3","ista":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 12, 6868.","mla":"Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer Nature, 2022, doi:10.1038/s41598-022-10827-3."},"year":"2022","abstract":[{"lang":"eng","text":"Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals."}],"date_updated":"2023-08-03T06:59:49Z","_id":"11344","article_number":"6868","oa":1,"publication_identifier":{"issn":["2045-2322"]},"status":"public","ec_funded":1,"month":"04","publication":"Scientific Reports","date_created":"2022-05-02T07:08:42Z","has_accepted_license":"1","department":[{"_id":"FyKo"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","volume":12,"quality_controlled":"1","external_id":{"pmid":["35477739"],"isi":["000788639400032"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","pmid":1,"acknowledgement":"The project was initiated with Aygul Minnegalieva and Yulia Yakovleva at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya, and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also thank Peter Vlasov for fruitful discussions.This study was supported by the Russian Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. ","file":[{"relation":"main_file","content_type":"application/pdf","file_size":3564155,"success":1,"checksum":"12601b8a5c6b83bb618f92bcb963ecc9","file_id":"11349","creator":"dernst","access_level":"open_access","date_updated":"2022-05-02T09:05:20Z","file_name":"2022_ScientificReports_Dranenko.pdf","date_created":"2022-05-02T09:05:20Z"}],"isi":1,"author":[{"full_name":"Dranenko, NO","first_name":"NO","last_name":"Dranenko"},{"full_name":"Tutukina, MN","first_name":"MN","last_name":"Tutukina"},{"full_name":"Gelfand, MS","first_name":"MS","last_name":"Gelfand"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga"}],"project":[{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature"},{"title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"06","pmid":1,"acknowledgement":"This work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank Noé Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.","file":[{"creator":"dernst","file_id":"11730","checksum":"af3f24d97c016d844df237abef987639","access_level":"open_access","date_updated":"2022-08-05T06:29:18Z","file_name":"2022_CurrentBiology_Nicolas.pdf","date_created":"2022-08-05T06:29:18Z","relation":"main_file","content_type":"application/pdf","file_size":12827717,"success":1}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"author":[{"first_name":"William J.","last_name":"Nicolas","full_name":"Nicolas, William J."},{"first_name":"Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"full_name":"Dutka, Przemysław","first_name":"Przemysław","last_name":"Dutka"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"},{"last_name":"Jensen","first_name":"Grant","full_name":"Jensen, Grant"},{"full_name":"Meyerowitz, Elliot","last_name":"Meyerowitz","first_name":"Elliot"}],"isi":1,"article_type":"original","article_processing_charge":"No","external_id":{"isi":["000822399200019"],"pmid":["35508170"]},"volume":32,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"quality_controlled":"1","date_created":"2022-05-04T06:22:06Z","page":"P2375-2389","publication":"Current Biology","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"type":"journal_article","oa":1,"publication_identifier":{"issn":["0960-9822"]},"status":"public","month":"06","year":"2022","date_updated":"2023-08-03T07:05:36Z","abstract":[{"text":"One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.","lang":"eng"}],"issue":"11","_id":"11351","ddc":["570"],"file_date_updated":"2022-08-05T06:29:18Z","scopus_import":"1","citation":{"mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.","ista":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2022.04.024","chicago":"Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur, Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","ieee":"W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz, “Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks,” Current Biology, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","ama":"Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389. doi:10.1016/j.cub.2022.04.024"},"intvolume":" 32","publication_status":"published","doi":"10.1016/j.cub.2022.04.024","date_published":"2022-06-06T00:00:00Z","oa_version":"Published Version"},{"external_id":{"isi":["000789316700001"]},"quality_controlled":"1","volume":3,"article_type":"original","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"has_accepted_license":"1","date_created":"2022-05-08T22:01:43Z","publication":"PRX Quantum","publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Dissipative quantum feedback in measurements using a parametrically coupled microcavity","project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"}],"author":[{"first_name":"Liu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","full_name":"Qiu, Liu"},{"full_name":"Huang, Guanhao","last_name":"Huang","first_name":"Guanhao"},{"full_name":"Shomroni, Itay","last_name":"Shomroni","first_name":"Itay"},{"last_name":"Pan","first_name":"Jiahe","full_name":"Pan, Jiahe"},{"first_name":"Paul","last_name":"Seidler","full_name":"Seidler, Paul"},{"full_name":"Kippenberg, Tobias J.","first_name":"Tobias J.","last_name":"Kippenberg"}],"isi":1,"file":[{"success":1,"file_size":1657177,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","checksum":"35ff9ddf1d54f64432e435b660edaeb6","file_id":"11358","date_created":"2022-05-09T07:10:51Z","date_updated":"2022-05-09T07:10:51Z","file_name":"2022_PRXQuantum_Qiu.pdf"}],"acknowledgement":"L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel, P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further supported by Swiss National Science Foundation under Grant Agreements No. 185870 (Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology (CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"13","citation":{"chicago":"Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/PRXQuantum.3.020309.","mla":"Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” PRX Quantum, vol. 3, no. 2, 020309, American Physical Society, 2022, doi:10.1103/PRXQuantum.3.020309.","apa":"Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., & Kippenberg, T. J. (2022). Dissipative quantum feedback in measurements using a parametrically coupled microcavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.3.020309","ista":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. PRX Quantum. 3(2), 020309.","ama":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. PRX Quantum. 2022;3(2). doi:10.1103/PRXQuantum.3.020309","ieee":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative quantum feedback in measurements using a parametrically coupled microcavity,” PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.","short":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum 3 (2022)."},"intvolume":" 3","scopus_import":"1","file_date_updated":"2022-05-09T07:10:51Z","ddc":["530"],"oa_version":"Published Version","date_published":"2022-04-13T00:00:00Z","publication_status":"published","doi":"10.1103/PRXQuantum.3.020309","month":"04","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"eissn":["26913399"]},"article_number":"020309","_id":"11353","date_updated":"2023-08-03T07:05:00Z","abstract":[{"text":"Micro- and nanoscale optical or microwave cavities are used in a wide range of classical applications and quantum science experiments, ranging from precision measurements, laser technologies to quantum control of mechanical motion. The dissipative photon loss via absorption, present to some extent in any optical cavity, is known to introduce thermo-optical effects and thereby impose fundamental limits on precision measurements. Here, we theoretically and experimentally reveal that such dissipative photon absorption can result in quantum feedback via in-loop field detection of the absorbed optical field, leading to the intracavity field fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum feedback to the cavity field arises. Strikingly, this modifies the optical cavity susceptibility in coherent response measurements (capable of both increasing or decreasing the bare cavity linewidth) and causes excess noise and correlations in incoherent interferometric optomechanical measurements using a cavity, that is parametrically coupled to a mechanical oscillator. We experimentally observe such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled optomechanical crystal cavitiess at both cryogenic temperature (approximately 8 K) and ambient conditions. The dissipative feedback introduces effective modifications to the optical cavity linewidth and the optomechanical scattering rate and gives rise to excess imprecision noise in the interferometric quantum measurement of mechanical motion. Such dissipative feedback differs fundamentally from a quantum nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback itself always results in an antisqueezed out-of-loop optical field, while it can enhance the coexisting Kerr squeezing under certain conditions. Our result applies to cavity spectroscopy in both optical and superconducting microwave cavities, and equally applies to any dissipative feedback mechanism of different bandwidth inside the cavity. It has wide-ranging implications for future dissipation engineering, such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency conversion, and nonreciprocity in photonic systems.","lang":"eng"}],"issue":"2","year":"2022"},{"department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Annals of Probability","page":"591-648","date_created":"2022-05-08T22:01:44Z","quality_controlled":"1","volume":50,"external_id":{"arxiv":["1811.11598"],"isi":["000773518500005"]},"article_processing_charge":"No","article_type":"original","author":[{"full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","orcid":"0000-0002-9881-6870"}],"isi":1,"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"day":"01","acknowledgement":"Research supported by the Sonderforschungsbereich 1060 and the Hausdorff Center for Mathematics. The author gratefully acknowledges funding of his current position at IST Austria by the Austrian Science Fund (FWF) grant F65 and by the European Research Council (ERC, Grant agreement No. 716117, awarded to Prof. Dr. Jan Maas).","title":"The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Mathematical Statistics","date_published":"2022-03-01T00:00:00Z","oa_version":"Preprint","doi":"10.1214/21-AOP1541","publication_status":"published","intvolume":" 50","citation":{"ama":"Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. Annals of Probability. 2022;50(2):591-648. doi:10.1214/21-AOP1541","ieee":"L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold,” Annals of Probability, vol. 50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022.","short":"L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.","apa":"Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-AOP1541","ista":"Dello Schiavo L. 2022. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. Annals of Probability. 50(2), 591–648.","mla":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” Annals of Probability, vol. 50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:10.1214/21-AOP1541.","chicago":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” Annals of Probability. Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AOP1541."},"scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1811.11598","open_access":"1"}],"_id":"11354","year":"2022","abstract":[{"lang":"eng","text":"We construct a recurrent diffusion process with values in the space of probability measures over an arbitrary closed Riemannian manifold of dimension d≥2. The process is associated with the Dirichlet form defined by integration of the Wasserstein gradient w.r.t. the Dirichlet–Ferguson measure, and is the counterpart on multidimensional base spaces to the modified massive Arratia flow over the unit interval described in V. Konarovskyi and M.-K. von Renesse (Comm. Pure Appl. Math. 72 (2019) 764–800). Together with two different constructions of the process, we discuss its ergodicity, invariant sets, finite-dimensional approximations, and Varadhan short-time asymptotics."}],"issue":"2","arxiv":1,"date_updated":"2023-10-17T12:50:24Z","ec_funded":1,"month":"03","oa":1,"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"status":"public"},{"type":"conference","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Fundamental Approaches to Software Engineering","page":"3-22","date_created":"2022-05-08T22:01:44Z","quality_controlled":"1","volume":13241,"external_id":{"isi":["000782393600001"]},"article_processing_charge":"No","author":[{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"full_name":"Da Costa, Ana Oliveira","first_name":"Ana Oliveira","last_name":"Da Costa"}],"isi":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"file":[{"access_level":"open_access","file_id":"11357","checksum":"7f6f860b20b8de2a249e9c1b4eee15cf","creator":"dernst","date_created":"2022-05-09T06:52:44Z","file_name":"2022_LNCS_Bartocci.pdf","date_updated":"2022-05-09T06:52:44Z","success":1,"file_size":479146,"content_type":"application/pdf","relation":"main_file"}],"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 956123 and was funded in part by the FWF project W1255-N23 and by the ERC-2020-AdG 101020093.","day":"29","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LNCS"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"Information-flow interfaces","oa_version":"Published Version","date_published":"2022-03-29T00:00:00Z","doi":"10.1007/978-3-030-99429-7_1","conference":{"start_date":"2022-04-02","name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2022-04-07","location":"Munich, Germany"},"publication_status":"published","intvolume":" 13241","citation":{"mla":"Bartocci, Ezio, et al. “Information-Flow Interfaces.” Fundamental Approaches to Software Engineering, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:10.1007/978-3-030-99429-7_1.","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Information-flow interfaces. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13241, 3–22.","apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa, A. O. (2022). Information-flow interfaces. In Fundamental Approaches to Software Engineering (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-99429-7_1","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Information-Flow Interfaces.” In Fundamental Approaches to Software Engineering, 13241:3–22. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-99429-7_1.","short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2022, pp. 3–22.","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Information-flow interfaces,” in Fundamental Approaches to Software Engineering, Munich, Germany, 2022, vol. 13241, pp. 3–22.","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow interfaces. In: Fundamental Approaches to Software Engineering. Vol 13241. Springer Nature; 2022:3-22. doi:10.1007/978-3-030-99429-7_1"},"scopus_import":"1","file_date_updated":"2022-05-09T06:52:44Z","ddc":["000"],"_id":"11355","abstract":[{"lang":"eng","text":"Contract-based design is a promising methodology for taming the complexity of developing sophisticated systems. A formal contract distinguishes between assumptions, which are constraints that the designer of a component puts on the environments in which the component can be used safely, and guarantees, which are promises that the designer asks from the team that implements the component. A theory of formal contracts can be formalized as an interface theory, which supports the composition and refinement of both assumptions and guarantees.\r\nAlthough there is a rich landscape of contract-based design methods that address functional and extra-functional properties, we present the first interface theory that is designed for ensuring system-wide security properties. Our framework provides a refinement relation and a composition operation that support both incremental design and independent implementability. We develop our theory for both stateless and stateful interfaces. We illustrate the applicability of our framework with an example inspired from the automotive domain."}],"date_updated":"2023-08-03T07:03:40Z","year":"2022","month":"03","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"isbn":["9783030994280"],"eissn":["1611-3349"],"issn":["0302-9743"]}},{"title":"Distinct electron and hole transports in SnSe crystals","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"isi":1,"author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","orcid":"0000-0002-9515-4277","first_name":"Cheng","full_name":"Chang, Cheng"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"full_name":"Su, Lizhong","last_name":"Su","first_name":"Lizhong"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"day":"15","acknowledgement":"This work was supported by the National Science Fund for Distinguished Young Scholars (51925101), National Key Research and Development Program of China (2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).","external_id":{"isi":["000835291100006"]},"volume":67,"quality_controlled":"1","article_processing_charge":"No","article_type":"letter_note","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"type":"journal_article","date_created":"2022-05-08T22:01:44Z","page":"1105-1107","publication":"Science Bulletin","month":"06","publication_identifier":{"eissn":["2095-9281"],"issn":["2095-9273"]},"oa":1,"status":"public","_id":"11356","year":"2022","date_updated":"2023-08-03T07:04:10Z","issue":"11","citation":{"ieee":"C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports in SnSe crystals,” Science Bulletin, vol. 67, no. 11. Elsevier, pp. 1105–1107, 2022.","ama":"Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 2022;67(11):1105-1107. doi:10.1016/j.scib.2022.04.007","short":"C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.","chicago":"Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron and Hole Transports in SnSe Crystals.” Science Bulletin. Elsevier, 2022. https://doi.org/10.1016/j.scib.2022.04.007.","ista":"Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 67(11), 1105–1107.","apa":"Chang, C., Qin, B., Su, L., & Zhao, L. D. (2022). Distinct electron and hole transports in SnSe crystals. Science Bulletin. Elsevier. https://doi.org/10.1016/j.scib.2022.04.007","mla":"Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.” Science Bulletin, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:10.1016/j.scib.2022.04.007."},"intvolume":" 67","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.scib.2022.04.007"}],"date_published":"2022-06-15T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.scib.2022.04.007"},{"title":"Learning verifiable representations","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"day":"12","file":[{"file_id":"11378","creator":"mlechner","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","access_level":"closed","date_updated":"2022-05-13T12:49:00Z","file_name":"src.zip","date_created":"2022-05-13T12:33:26Z","relation":"source_file","content_type":"application/zip","file_size":13210143},{"date_created":"2022-05-16T08:02:28Z","date_updated":"2022-05-17T15:19:39Z","file_name":"thesis_main-a2.pdf","access_level":"open_access","file_id":"11382","creator":"mlechner","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","file_size":2732536,"relation":"main_file","content_type":"application/pdf"}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11366"},{"id":"7808","relation":"part_of_dissertation","status":"public"},{"id":"10666","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10665"},{"relation":"part_of_dissertation","status":"public","id":"10667"}]},"keyword":["neural networks","verification","machine learning"],"date_created":"2022-05-12T07:14:01Z","page":"124","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"type":"dissertation","publication_identifier":{"isbn":["978-3-99078-017-6"]},"oa":1,"status":"public","ec_funded":1,"month":"05","year":"2022","date_updated":"2025-07-14T09:10:11Z","abstract":[{"lang":"eng","text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks."}],"_id":"11362","ddc":["004"],"file_date_updated":"2022-05-17T15:19:39Z","citation":{"ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","mla":"Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.","apa":"Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","ama":"Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362"},"publication_status":"published","doi":"10.15479/at:ista:11362","date_published":"2022-05-12T00:00:00Z","oa_version":"Published Version"},{"ec_funded":1,"month":"04","oa":1,"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"11366","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"article_number":"2204.07373","year":"2022","day":"15","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not\r\ncome for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off\r\nbut inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in\r\nconjunction with adversarial robot learning can make adversarial training suitable for real-world robot applications. We evaluate a wide variety of robot learning tasks ranging from autonomous driving in a high-fidelity environment\r\namenable to sim-to-real deployment, to mobile robot gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative side-effects caused by\r\nadversarial training still outweigh the improvements by an order of magnitude. We conclude that more substantial advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"acknowledgement":"This work was supported in parts by the ERC-2020-AdG 101020093, National Science Foundation (NSF), and JP\r\nMorgan Graduate Fellowships. We thank Christoph Lampert for inspiring this work.\r\n","arxiv":1,"date_updated":"2023-08-01T13:36:50Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11362"},{"status":"public","relation":"later_version","id":"12704"}]},"citation":{"ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv. doi:10.48550/arXiv.2204.07373","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” arXiv. .","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.).","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2204.07373.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (n.d.). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv. https://doi.org/10.48550/arXiv.2204.07373","ista":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv, 2204.07373.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” ArXiv, 2204.07373, doi:10.48550/arXiv.2204.07373."},"external_id":{"arxiv":["2204.07373"]},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.07373"}],"date_published":"2022-04-15T00:00:00Z","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","type":"preprint","publication":"arXiv","date_created":"2022-05-12T13:20:17Z","doi":"10.48550/arXiv.2204.07373","publication_status":"submitted"},{"status":"public","oa":1,"publication_identifier":{"issn":["2041-1723"]},"month":"05","ec_funded":1,"abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"date_updated":"2024-02-21T12:35:18Z","year":"2022","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_number":"2635","_id":"11373","scopus_import":"1","file_date_updated":"2022-05-13T09:10:51Z","ddc":["570"],"intvolume":" 13","citation":{"chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-30301-y.","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., & Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-30301-y","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Nature Communications, vol. 13, 2635, Springer Nature, 2022, doi:10.1038/s41467-022-30301-y.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","ieee":"P. Radler et al., “In vitro reconstitution of Escherichia coli divisome activation,” Nature Communications, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 2022;13. doi:10.1038/s41467-022-30301-y","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022)."},"doi":"10.1038/s41467-022-30301-y","publication_status":"published","oa_version":"Published Version","date_published":"2022-05-12T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"In vitro reconstitution of Escherichia coli divisome activation","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","day":"12","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp"},{"full_name":"Baranova, Natalia S.","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Michalik, David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","last_name":"Michalik","first_name":"David"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"isi":1,"project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":6945191,"success":1,"creator":"dernst","file_id":"11374","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","access_level":"open_access","date_updated":"2022-05-13T09:10:51Z","file_name":"2022_NatureCommunications_Radler.pdf","date_created":"2022-05-13T09:10:51Z"}],"article_processing_charge":"No","article_type":"original","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"quality_controlled":"1","volume":13,"external_id":{"isi":["000795171100037"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14280"},{"status":"public","relation":"research_data","id":"10934"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}]},"has_accepted_license":"1","publication":"Nature Communications","date_created":"2022-05-13T09:06:28Z","type":"journal_article","department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}]},{"_id":"11379","year":"2022","arxiv":1,"abstract":[{"lang":"eng","text":"Bernal-stacked multilayer graphene is a versatile platform to explore quantum transport phenomena and interaction physics due to its exceptional tunability via electrostatic gating. For instance, upon applying a perpendicular electric field, its band structure exhibits several off-center Dirac points (so-called Dirac gullies) in each valley. Here, the formation of Dirac gullies and the interaction-induced breakdown of gully coherence is explored via magnetotransport measurements in high-quality Bernal-stacked (ABA) trilayer graphene. At zero magnetic field, multiple Lifshitz transitions indicating the formation of Dirac gullies are identified. In the quantum Hall regime, the emergence of Dirac gullies is evident as an increase in Landau level degeneracy. When tuning both electric and magnetic fields, electron–electron interactions can be controllably enhanced until, beyond critical electric and magnetic fields, the gully degeneracy is eventually lifted. The arising correlated ground state is consistent with a previously predicted nematic phase that spontaneously breaks the rotational gully symmetry."}],"issue":"8","date_updated":"2023-08-03T07:12:45Z","month":"04","oa":1,"publication_identifier":{"issn":["15306984"],"eissn":["15306992"]},"status":"public","date_published":"2022-04-27T00:00:00Z","oa_version":"Preprint","doi":"10.1021/acs.nanolett.2c00435","publication_status":"published","intvolume":" 22","citation":{"apa":"Winterer, F., Seiler, A. M., Ghazaryan, A., Geisenhof, F. R., Watanabe, K., Taniguchi, T., … Weitz, R. T. (2022). Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.2c00435","ista":"Winterer F, Seiler AM, Ghazaryan A, Geisenhof FR, Watanabe K, Taniguchi T, Serbyn M, Weitz RT. 2022. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. Nano Letters. 22(8), 3317–3322.","mla":"Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” Nano Letters, vol. 22, no. 8, American Chemical Society, 2022, pp. 3317–22, doi:10.1021/acs.nanolett.2c00435.","chicago":"Winterer, Felix, Anna M. Seiler, Areg Ghazaryan, Fabian R. Geisenhof, Kenji Watanabe, Takashi Taniguchi, Maksym Serbyn, and R. Thomas Weitz. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” Nano Letters. American Chemical Society, 2022. https://doi.org/10.1021/acs.nanolett.2c00435.","short":"F. Winterer, A.M. Seiler, A. Ghazaryan, F.R. Geisenhof, K. Watanabe, T. Taniguchi, M. Serbyn, R.T. Weitz, Nano Letters 22 (2022) 3317–3322.","ieee":"F. Winterer et al., “Spontaneous gully-polarized quantum hall states in ABA trilayer graphene,” Nano Letters, vol. 22, no. 8. American Chemical Society, pp. 3317–3322, 2022.","ama":"Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. Nano Letters. 2022;22(8):3317-3322. doi:10.1021/acs.nanolett.2c00435"},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00556"}],"scopus_import":"1","author":[{"last_name":"Winterer","first_name":"Felix","full_name":"Winterer, Felix"},{"full_name":"Seiler, Anna M.","first_name":"Anna M.","last_name":"Seiler"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543"},{"first_name":"Fabian R.","last_name":"Geisenhof","full_name":"Geisenhof, Fabian R."},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Weitz, R. Thomas","last_name":"Weitz","first_name":"R. Thomas"}],"isi":1,"day":"27","acknowledgement":"We acknowledge funding from the Center for Nanoscience (CeNS) and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy-EXC-2111-390814868 (MCQST). K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan (Grant Number PMXP0112101001) and JSPS KAKENHI (Grant Numbers 19H05790 and JP20H00354).","title":"Spontaneous gully-polarized quantum hall states in ABA trilayer graphene","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Nano Letters","page":"3317-3322","date_created":"2022-05-15T22:01:41Z","quality_controlled":"1","volume":22,"external_id":{"isi":["000809056900019"],"arxiv":["2109.00556"]},"article_processing_charge":"No","article_type":"original"},{"article_processing_charge":"No","related_material":{"record":[{"id":"6713","relation":"part_of_dissertation","status":"public"}]},"has_accepted_license":"1","page":"98","date_created":"2022-05-16T16:49:18Z","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","supervisor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"day":"18","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy"}],"file":[{"file_size":8247240,"embargo":"2023-05-19","relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"4d75e6a619df7e8a9d6e840aee182380","file_id":"11398","creator":"sbelohla","date_created":"2022-05-19T13:03:13Z","file_name":"thesis_sb_final_pdfa.pdf","date_updated":"2023-05-20T22:30:03Z"},{"checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","file_id":"11399","creator":"sbelohla","access_level":"closed","date_updated":"2023-05-20T22:30:03Z","file_name":"thesis_sb_final.zip","date_created":"2022-05-19T13:07:47Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","file_size":7094}],"file_date_updated":"2023-05-20T22:30:03Z","ddc":["576"],"citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022."},"publication_status":"published","doi":"10.15479/at:ista:11388","oa_version":"Published Version","date_published":"2022-05-18T00:00:00Z","status":"public","oa":1,"publication_identifier":{"isbn":["978-3-99078-018-3"]},"month":"05","date_updated":"2023-08-29T06:41:51Z","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"year":"2022","_id":"11388"},{"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"type":"dissertation","page":"108","date_created":"2022-05-17T08:57:41Z","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7391"}]},"article_processing_charge":"No","file":[{"checksum":"8fc695d88020d70d231dad0e9f10b138","creator":"cchlebak","file_id":"11395","access_level":"closed","date_updated":"2023-05-17T22:30:03Z","file_name":"MJ thesis.docx","date_created":"2022-05-17T09:08:06Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":56427603},{"file_name":"MJ_thesis_PDFA.pdf","date_updated":"2023-05-17T22:30:03Z","date_created":"2022-05-17T12:09:25Z","creator":"cchlebak","file_id":"11397","checksum":"c1dd20a1aece521b3500607b00e463d6","access_level":"open_access","content_type":"application/pdf","relation":"main_file","embargo":"2023-05-16","file_size":4351981}],"author":[{"full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","first_name":"Marijo"}],"day":"16","supervisor":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-05-16T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.15479/at:ista:11393","citation":{"short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:10.15479/at:ista:11393","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11393.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","apa":"Jevtic, M. (2022). Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11393","mla":"Jevtic, Marijo. Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11393."},"ddc":["570"],"file_date_updated":"2023-05-17T22:30:03Z","_id":"11393","acknowledged_ssus":[{"_id":"EM-Fac"}],"year":"2022","date_updated":"2023-09-07T14:53:44Z","abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"month":"05","oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public"},{"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"status":"public","ec_funded":1,"month":"05","year":"2022","abstract":[{"lang":"eng","text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes."}],"issue":"19","date_updated":"2023-09-05T11:59:00Z","_id":"11400","article_number":"194902","ddc":["540"],"file_date_updated":"2022-05-23T07:45:33Z","intvolume":" 156","citation":{"ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:10.1063/5.0087769.","apa":"Palaia, I., & Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0087769","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0087769.","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” The Journal of Chemical Physics, vol. 156, no. 19. AIP Publishing, 2022.","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 2022;156(19). doi:10.1063/5.0087769","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022)."},"doi":"10.1063/5.0087769","publication_status":"published","date_published":"2022-05-16T00:00:00Z","oa_version":"Published Version","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"AIP Publishing","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"16","acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","file":[{"content_type":"application/pdf","relation":"main_file","file_size":6387208,"success":1,"checksum":"7fada58059676a4bb0944b82247af740","creator":"dernst","file_id":"11405","access_level":"open_access","file_name":"2022_JourChemPhysics_Palaia.pdf","date_updated":"2022-05-23T07:45:33Z","date_created":"2022-05-23T07:45:33Z"}],"isi":1,"author":[{"orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"article_type":"original","article_processing_charge":"No","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"volume":156,"quality_controlled":"1","external_id":{"isi":["000797236000004"]},"publication":"The Journal of Chemical Physics","date_created":"2022-05-22T17:04:48Z","has_accepted_license":"1","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"type":"journal_article"}]