[{"month":"04","pmid":1,"ddc":["570"],"file_date_updated":"2022-05-02T09:05:20Z","citation":{"ieee":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","apa":"Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>","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.","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. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>","chicago":"Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>.","mla":"Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>."},"day":"27","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11349","date_created":"2022-05-02T09:05:20Z","file_name":"2022_ScientificReports_Dranenko.pdf","file_size":3564155,"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"12601b8a5c6b83bb618f92bcb963ecc9","success":1,"date_updated":"2022-05-02T09:05:20Z"}],"article_processing_charge":"No","volume":12,"has_accepted_license":"1","_id":"11344","title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","author":[{"first_name":"NO","last_name":"Dranenko","full_name":"Dranenko, NO"},{"first_name":"MN","last_name":"Tutukina","full_name":"Tutukina, MN"},{"full_name":"Gelfand, MS","last_name":"Gelfand","first_name":"MS"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva"}],"doi":"10.1038/s41598-022-10827-3","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."}],"project":[{"grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"issn":["2045-2322"]},"ec_funded":1,"publication_status":"published","status":"public","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. ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"date_created":"2022-05-02T07:08:42Z","scopus_import":"1","date_published":"2022-04-27T00:00:00Z","external_id":{"pmid":["35477739"],"isi":["000788639400032"]},"publisher":"Springer Nature","intvolume":"        12","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"oa":1,"year":"2022","date_updated":"2023-08-03T06:59:49Z","publication":"Scientific Reports","article_number":"6868","article_type":"original"},{"file":[{"date_created":"2022-08-05T06:29:18Z","file_id":"11730","relation":"main_file","creator":"dernst","file_size":12827717,"file_name":"2022_CurrentBiology_Nicolas.pdf","date_updated":"2022-08-05T06:29:18Z","success":1,"content_type":"application/pdf","checksum":"af3f24d97c016d844df237abef987639","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":32,"citation":{"mla":"Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.” <i>Current Biology</i>, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>.","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.” <i>Current Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>.","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,” <i>Current Biology</i>, vol. 32, no. 11. Elsevier, pp. P2375-2389, 2022.","apa":"Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., &#38; Meyerowitz, E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">https://doi.org/10.1016/j.cub.2022.04.024</a>","short":"W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz, Current Biology 32 (2022) P2375-2389.","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.","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. <i>Current Biology</i>. 2022;32(11):P2375-2389. doi:<a href=\"https://doi.org/10.1016/j.cub.2022.04.024\">10.1016/j.cub.2022.04.024</a>"},"day":"06","month":"06","file_date_updated":"2022-08-05T06:29:18Z","ddc":["570"],"pmid":1,"oa_version":"Published Version","publication_identifier":{"issn":["0960-9822"]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"publication_status":"published","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.","status":"public","title":"Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks","author":[{"first_name":"William J.","full_name":"Nicolas, William J.","last_name":"Nicolas"},{"orcid":"0000-0001-7149-769X","last_name":"Fäßler","full_name":"Fäßler, Florian","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Przemysław","last_name":"Dutka","full_name":"Dutka, Przemysław"},{"orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jensen","full_name":"Jensen, Grant","first_name":"Grant"},{"first_name":"Elliot","full_name":"Meyerowitz, Elliot","last_name":"Meyerowitz"}],"_id":"11351","abstract":[{"lang":"eng","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."}],"issue":"11","doi":"10.1016/j.cub.2022.04.024","publisher":"Elsevier","intvolume":"        32","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"FlSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-06T00:00:00Z","external_id":{"pmid":["35508170"],"isi":["000822399200019"]},"date_created":"2022-05-04T06:22:06Z","scopus_import":"1","publication":"Current Biology","date_updated":"2023-08-03T07:05:36Z","page":"P2375-2389","article_type":"original","oa":1,"year":"2022","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2022-05-09T07:10:51Z","access_level":"open_access","content_type":"application/pdf","checksum":"35ff9ddf1d54f64432e435b660edaeb6","file_name":"2022_PRXQuantum_Qiu.pdf","relation":"main_file","creator":"dernst","file_size":1657177,"file_id":"11358","date_created":"2022-05-09T07:10:51Z"}],"has_accepted_license":"1","volume":3,"article_processing_charge":"No","day":"13","citation":{"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,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","apa":"Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., &#38; Kippenberg, T. J. (2022). Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>","ama":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>","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.","short":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum 3 (2022).","mla":"Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” <i>PRX Quantum</i>, vol. 3, no. 2, 020309, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>.","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.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>."},"file_date_updated":"2022-05-09T07:10:51Z","month":"04","ddc":["530"],"oa_version":"Published Version","publication_identifier":{"eissn":["26913399"]},"project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"}],"status":"public","publication_status":"published","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.","ec_funded":1,"author":[{"orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","first_name":"Liu","full_name":"Qiu, Liu","last_name":"Qiu"},{"first_name":"Guanhao","full_name":"Huang, Guanhao","last_name":"Huang"},{"full_name":"Shomroni, Itay","last_name":"Shomroni","first_name":"Itay"},{"first_name":"Jiahe","full_name":"Pan, Jiahe","last_name":"Pan"},{"last_name":"Seidler","full_name":"Seidler, Paul","first_name":"Paul"},{"last_name":"Kippenberg","full_name":"Kippenberg, Tobias J.","first_name":"Tobias J."}],"title":"Dissipative quantum feedback in measurements using a parametrically coupled microcavity","_id":"11353","issue":"2","abstract":[{"lang":"eng","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."}],"doi":"10.1103/PRXQuantum.3.020309","intvolume":"         3","publisher":"American Physical Society","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"JoFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000789316700001"]},"date_published":"2022-04-13T00:00:00Z","scopus_import":"1","date_created":"2022-05-08T22:01:43Z","publication":"PRX Quantum","date_updated":"2023-08-03T07:05:00Z","article_type":"original","article_number":"020309","oa":1,"year":"2022"},{"date_created":"2022-05-08T22:01:44Z","scopus_import":"1","date_published":"2022-03-01T00:00:00Z","external_id":{"isi":["000773518500005"],"arxiv":["1811.11598"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Institute of Mathematical Statistics","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.11598"}],"intvolume":"        50","year":"2022","oa":1,"page":"591-648","article_type":"original","date_updated":"2023-10-17T12:50:24Z","publication":"Annals of Probability","oa_version":"Preprint","month":"03","citation":{"short":"L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.","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.","ama":"Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. 2022;50(2):591-648. doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>","ieee":"L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold,” <i>Annals of Probability</i>, vol. 50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022.","apa":"Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>","mla":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>, vol. 50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>.","chicago":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>."},"day":"01","article_processing_charge":"No","volume":50,"arxiv":1,"doi":"10.1214/21-AOP1541","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","_id":"11354","title":"The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870"}],"ec_funded":1,"status":"public","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).","publication_status":"published","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]}},{"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","intvolume":"     13241","publisher":"Springer Nature","date_published":"2022-03-29T00:00:00Z","external_id":{"isi":["000782393600001"]},"scopus_import":"1","date_created":"2022-05-08T22:01:44Z","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"3-22","publication":"Fundamental Approaches to Software Engineering","date_updated":"2023-08-03T07:03:40Z","alternative_title":["LNCS"],"year":"2022","oa":1,"has_accepted_license":"1","article_processing_charge":"No","volume":13241,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2022-05-09T06:52:44Z","access_level":"open_access","content_type":"application/pdf","checksum":"7f6f860b20b8de2a249e9c1b4eee15cf","file_name":"2022_LNCS_Bartocci.pdf","file_size":479146,"creator":"dernst","relation":"main_file","file_id":"11357","date_created":"2022-05-09T06:52:44Z"}],"conference":{"name":"FASE: Fundamental Approaches to Software Engineering","location":"Munich, Germany","start_date":"2022-04-02","end_date":"2022-04-07"},"oa_version":"Published Version","day":"29","citation":{"apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Information-flow interfaces. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Information-flow interfaces,” in <i>Fundamental Approaches to Software Engineering</i>, Munich, Germany, 2022, vol. 13241, pp. 3–22.","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.","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.","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow interfaces. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13241. Springer Nature; 2022:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>","mla":"Bartocci, Ezio, et al. “Information-Flow Interfaces.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>.","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Information-Flow Interfaces.” In <i>Fundamental Approaches to Software Engineering</i>, 13241:3–22. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>."},"month":"03","file_date_updated":"2022-05-09T06:52:44Z","ddc":["000"],"publication_status":"published","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.","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030994280"],"issn":["0302-9743"]},"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"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."}],"doi":"10.1007/978-3-030-99429-7_1","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"first_name":"Ana Oliveira","last_name":"Da Costa","full_name":"Da Costa, Ana Oliveira"}],"title":"Information-flow interfaces","_id":"11355"},{"date_updated":"2023-08-03T07:04:10Z","publication":"Science Bulletin","page":"1105-1107","article_type":"letter_note","oa":1,"year":"2022","publisher":"Elsevier","intvolume":"        67","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.scib.2022.04.007"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaIb"}],"date_created":"2022-05-08T22:01:44Z","scopus_import":"1","external_id":{"isi":["000835291100006"]},"date_published":"2022-06-15T00:00:00Z","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"publication_identifier":{"issn":["2095-9273"],"eissn":["2095-9281"]},"status":"public","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).","publication_status":"published","_id":"11356","title":"Distinct electron and hole transports in SnSe crystals","author":[{"orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang"},{"first_name":"Bingchao","full_name":"Qin, Bingchao","last_name":"Qin"},{"first_name":"Lizhong","last_name":"Su","full_name":"Su, Lizhong"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"}],"doi":"10.1016/j.scib.2022.04.007","issue":"11","volume":67,"article_processing_charge":"No","month":"06","citation":{"apa":"Chang, C., Qin, B., Su, L., &#38; Zhao, L. D. (2022). Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>","ieee":"C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports in SnSe crystals,” <i>Science Bulletin</i>, 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. <i>Science Bulletin</i>. 2022;67(11):1105-1107. doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>","ista":"Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 67(11), 1105–1107.","short":"C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.","mla":"Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>.","chicago":"Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>."},"day":"15","oa_version":"Published Version"},{"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-05-12T00:00:00Z","date_created":"2022-05-12T07:14:01Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"keyword":["neural networks","verification","machine learning"],"date_updated":"2025-07-14T09:10:11Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11366"},{"status":"public","relation":"part_of_dissertation","id":"7808"},{"id":"10666","status":"public","relation":"part_of_dissertation"},{"id":"10665","relation":"part_of_dissertation","status":"public"},{"id":"10667","status":"public","relation":"part_of_dissertation"}]},"page":"124","citation":{"chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>.","mla":"Lechner, Mathias. <i>Learning Verifiable Representations</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","apa":"Lechner, M. (2022). <i>Learning verifiable representations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","ama":"Lechner M. Learning verifiable representations. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022."},"day":"12","month":"05","file_date_updated":"2022-05-17T15:19:39Z","ddc":["004"],"license":"https://creativecommons.org/licenses/by-nd/4.0/","oa_version":"Published Version","degree_awarded":"PhD","tmp":{"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)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"file":[{"date_created":"2022-05-13T12:33:26Z","file_id":"11378","date_updated":"2022-05-13T12:49:00Z","content_type":"application/zip","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","access_level":"closed","creator":"mlechner","relation":"source_file","file_size":13210143,"file_name":"src.zip"},{"creator":"mlechner","relation":"main_file","file_size":2732536,"file_name":"thesis_main-a2.pdf","content_type":"application/pdf","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","access_level":"open_access","date_updated":"2022-05-17T15:19:39Z","date_created":"2022-05-16T08:02:28Z","file_id":"11382"}],"has_accepted_license":"1","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"Learning verifiable representations","author":[{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"_id":"11362","abstract":[{"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.","lang":"eng"}],"doi":"10.15479/at:ista:11362","publication_identifier":{"isbn":["978-3-99078-017-6"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publication_status":"published","status":"public","ec_funded":1},{"doi":"10.48550/arXiv.2204.07373","year":"2022","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"}],"_id":"11366","author":[{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amini, Alexander","last_name":"Amini","first_name":"Alexander"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","oa":1,"ec_funded":1,"article_number":"2204.07373","publication_status":"submitted","status":"public","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","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11362"},{"relation":"later_version","status":"public","id":"12704"}]},"date_updated":"2023-08-01T13:36:50Z","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publication":"arXiv","date_created":"2022-05-12T13:20:17Z","oa_version":"Preprint","date_published":"2022-04-15T00:00:00Z","external_id":{"arxiv":["2204.07373"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","day":"15","department":[{"_id":"ToHe"}],"citation":{"short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.).","ista":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv, 2204.07373.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>","apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (n.d.). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>arXiv</i>. .","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, 2204.07373, doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>."},"language":[{"iso":"eng"}],"type":"preprint","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.07373","open_access":"1"}],"arxiv":1},{"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"intvolume":"        13","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"scopus_import":"1","date_created":"2022-05-13T09:06:28Z","date_published":"2022-05-12T00:00:00Z","external_id":{"isi":["000795171100037"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaLo"}],"article_type":"original","article_number":"2635","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-34485-1","relation":"erratum"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14280"},{"status":"public","relation":"research_data","id":"10934"}]},"date_updated":"2024-02-21T12:35:18Z","publication":"Nature Communications","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"year":"2022","oa":1,"article_processing_charge":"No","volume":13,"has_accepted_license":"1","file":[{"file_id":"11374","date_created":"2022-05-13T09:10:51Z","success":1,"date_updated":"2022-05-13T09:10:51Z","access_level":"open_access","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","content_type":"application/pdf","file_name":"2022_NatureCommunications_Radler.pdf","creator":"dernst","relation":"main_file","file_size":6945191}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["570"],"month":"05","file_date_updated":"2022-05-13T09:10:51Z","day":"12","citation":{"mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","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.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","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)."},"ec_funded":1,"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.","status":"public","publication_status":"published","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","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-30301-y","abstract":[{"lang":"eng","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."}],"_id":"11373","author":[{"last_name":"Radler","full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "},{"orcid":"0000-0002-3086-9124","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","full_name":"Baranova, Natalia S."},{"orcid":"0000-0001-6730-4461","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalik","full_name":"Michalik, David","first_name":"David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin"}],"title":"In vitro reconstitution of Escherichia coli divisome activation"},{"citation":{"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.” <i>Nano Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>.","mla":"Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” <i>Nano Letters</i>, vol. 22, no. 8, American Chemical Society, 2022, pp. 3317–22, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>.","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. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>","ieee":"F. Winterer <i>et al.</i>, “Spontaneous gully-polarized quantum hall states in ABA trilayer graphene,” <i>Nano Letters</i>, vol. 22, no. 8. American Chemical Society, pp. 3317–3322, 2022.","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.","ama":"Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. <i>Nano Letters</i>. 2022;22(8):3317-3322. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>","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."},"day":"27","month":"04","oa_version":"Preprint","arxiv":1,"volume":22,"article_processing_charge":"No","title":"Spontaneous gully-polarized quantum hall states in ABA trilayer graphene","author":[{"first_name":"Felix","last_name":"Winterer","full_name":"Winterer, Felix"},{"first_name":"Anna M.","last_name":"Seiler","full_name":"Seiler, Anna M."},{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"last_name":"Geisenhof","full_name":"Geisenhof, Fabian R.","first_name":"Fabian R."},{"last_name":"Watanabe","full_name":"Watanabe, Kenji","first_name":"Kenji"},{"last_name":"Taniguchi","full_name":"Taniguchi, Takashi","first_name":"Takashi"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"last_name":"Weitz","full_name":"Weitz, R. Thomas","first_name":"R. Thomas"}],"_id":"11379","abstract":[{"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.","lang":"eng"}],"issue":"8","doi":"10.1021/acs.nanolett.2c00435","publication_identifier":{"eissn":["15306992"],"issn":["15306984"]},"status":"public","publication_status":"published","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).","department":[{"_id":"MaSe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000809056900019"],"arxiv":["2109.00556"]},"date_published":"2022-04-27T00:00:00Z","date_created":"2022-05-15T22:01:41Z","scopus_import":"1","publisher":"American Chemical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.00556","open_access":"1"}],"intvolume":"        22","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","oa":1,"year":"2022","publication":"Nano Letters","date_updated":"2023-08-03T07:12:45Z","page":"3317-3322","article_type":"original"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-05-16T16:49:18Z","date_published":"2022-05-18T00:00:00Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"year":"2022","alternative_title":["ISTA Thesis"],"date_updated":"2023-08-29T06:41:51Z","page":"98","related_material":{"record":[{"id":"6713","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2023-05-20T22:30:03Z","month":"05","ddc":["576"],"citation":{"mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","short":"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:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>"},"day":"18","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11398","date_created":"2022-05-19T13:03:13Z","date_updated":"2023-05-20T22:30:03Z","access_level":"open_access","content_type":"application/pdf","checksum":"4d75e6a619df7e8a9d6e840aee182380","embargo":"2023-05-19","file_name":"thesis_sb_final_pdfa.pdf","relation":"main_file","creator":"sbelohla","file_size":8247240},{"date_created":"2022-05-19T13:07:47Z","file_id":"11399","embargo_to":"open_access","date_updated":"2023-05-20T22:30:03Z","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","content_type":"application/x-zip-compressed","access_level":"closed","file_size":7094,"creator":"sbelohla","relation":"source_file","file_name":"thesis_sb_final.zip"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"11388","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"author":[{"first_name":"Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X"}],"doi":"10.15479/at:ista:11388","abstract":[{"lang":"eng","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."}],"publication_identifier":{"isbn":["978-3-99078-018-3"]},"publication_status":"published","status":"public"},{"degree_awarded":"PhD","file":[{"date_updated":"2023-05-17T22:30:03Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"8fc695d88020d70d231dad0e9f10b138","file_name":"MJ thesis.docx","file_size":56427603,"creator":"cchlebak","relation":"source_file","file_id":"11395","date_created":"2022-05-17T09:08:06Z","embargo_to":"open_access"},{"checksum":"c1dd20a1aece521b3500607b00e463d6","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-05-17T22:30:03Z","creator":"cchlebak","relation":"main_file","file_size":4351981,"file_name":"MJ_thesis_PDFA.pdf","embargo":"2023-05-16","date_created":"2022-05-17T12:09:25Z","file_id":"11397"}],"has_accepted_license":"1","article_processing_charge":"No","day":"16","citation":{"mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","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. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","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.","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>","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.","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."},"ddc":["570"],"month":"05","file_date_updated":"2023-05-17T22:30:03Z","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","status":"public","author":[{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","first_name":"Marijo","full_name":"Jevtic, Marijo","last_name":"Jevtic"}],"supervisor":[{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"}],"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","_id":"11393","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"}],"doi":"10.15479/at:ista:11393","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-05-16T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2022-05-17T08:57:41Z","date_updated":"2023-09-07T14:53:44Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7391"}]},"page":"108","oa":1,"year":"2022","alternative_title":["ISTA Thesis"]},{"article_type":"original","article_number":"194902","publication":"The Journal of Chemical Physics","date_updated":"2023-09-05T11:59:00Z","year":"2022","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"oa":1,"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       156","publisher":"AIP Publishing","external_id":{"isi":["000797236000004"]},"date_published":"2022-05-16T00:00:00Z","date_created":"2022-05-22T17:04:48Z","department":[{"_id":"AnSa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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).","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"issue":"19","abstract":[{"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.","lang":"eng"}],"doi":"10.1063/5.0087769","author":[{"orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela"}],"title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","_id":"11400","has_accepted_license":"1","volume":156,"article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2022_JourChemPhysics_Palaia.pdf","relation":"main_file","file_size":6387208,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"7fada58059676a4bb0944b82247af740","success":1,"date_updated":"2022-05-23T07:45:33Z","file_id":"11405","date_created":"2022-05-23T07:45:33Z"}],"oa_version":"Published Version","day":"16","citation":{"apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","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.","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>."},"file_date_updated":"2022-05-23T07:45:33Z","month":"05","ddc":["540"]},{"volume":14,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"2022_NPGAsiaMaterials_Nguyen.pdf","creator":"dernst","relation":"main_file","file_size":6202545,"access_level":"open_access","checksum":"0579997cc1d28bf66e29357e08e3e39d","content_type":"application/pdf","success":1,"date_updated":"2022-05-23T06:47:57Z","file_id":"11404","date_created":"2022-05-23T06:47:57Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["540"],"month":"05","file_date_updated":"2022-05-23T06:47:57Z","day":"13","citation":{"mla":"Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>, vol. 14, 42, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>.","chicago":"Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>.","ieee":"V. Q. Nguyen <i>et al.</i>, “Unidentified major p-type source in SnSe: Multivacancies,” <i>NPG Asia Materials</i>, vol. 14. Springer Nature, 2022.","apa":"Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong, V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>","short":"V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T. Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022).","ama":"Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. 2022;14. doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>","ista":"Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies. NPG Asia Materials. 14, 42."},"publication_status":"published","status":"public","acknowledgement":"This work was supported by the National Research Foundation of Korea [NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].","publication_identifier":{"eissn":["1884-4057"],"issn":["1884-4049"]},"doi":"10.1038/s41427-022-00393-5","abstract":[{"lang":"eng","text":"Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower group dopants to achieve successful p-type doping in SnSe with high ZT values. A known, facile, and powerful alternative way to introduce a hole carrier is to use a natural single Sn vacancy, VSn. Through transport and scanning tunneling microscopy studies, we discovered that VSn are dominant in high-quality (slow cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and Vmulti help to increase the power factors of SnSe, whereas samples with dominant VSn have superior thermoelectric properties in SnSe single crystals. Additionally, the observation that Vmulti are good p-type sources observed in relatively low-quality single crystals is useful in thermoelectric applications because polycrystalline SnSe can be used due to its mechanical strength; this substance is usually fabricated at very high cooling speeds."}],"_id":"11401","author":[{"full_name":"Nguyen, Van Quang","last_name":"Nguyen","first_name":"Van Quang"},{"first_name":"Thi Ly","full_name":"Trinh, Thi Ly","last_name":"Trinh"},{"orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","full_name":"Chang, Cheng","last_name":"Chang"},{"last_name":"Zhao","full_name":"Zhao, Li Dong","first_name":"Li Dong"},{"first_name":"Thi Huong","last_name":"Nguyen","full_name":"Nguyen, Thi Huong"},{"first_name":"Van Thiet","last_name":"Duong","full_name":"Duong, Van Thiet"},{"last_name":"Duong","full_name":"Duong, Anh Tuan","first_name":"Anh Tuan"},{"full_name":"Park, Jong Ho","last_name":"Park","first_name":"Jong Ho"},{"first_name":"Sudong","full_name":"Park, Sudong","last_name":"Park"},{"last_name":"Kim","full_name":"Kim, Jungdae","first_name":"Jungdae"},{"first_name":"Sunglae","last_name":"Cho","full_name":"Cho, Sunglae"}],"title":"Unidentified major p-type source in SnSe: Multivacancies","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"        14","publisher":"Springer Nature","scopus_import":"1","date_created":"2022-05-22T22:01:40Z","external_id":{"isi":["000794880200001"]},"date_published":"2022-05-13T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaIb"}],"article_type":"original","article_number":"42","date_updated":"2023-08-03T07:13:58Z","publication":"NPG Asia Materials","year":"2022","oa":1},{"arxiv":1,"volume":129,"article_processing_charge":"No","month":"11","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>, vol. 129, Elsevier, 2022, pp. 1–21, doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>.","ista":"Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon. Journal of Computer and System Sciences. 129, 1–21.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. 2022;129:1-21. doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>","short":"K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022) 1–21.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” <i>Journal of Computer and System Sciences</i>, vol. 129. Elsevier, pp. 1–21, 2022.","apa":"Chatterjee, K., &#38; Doyen, L. (2022). Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>"},"day":"01","oa_version":"Preprint","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"This work was partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).","_id":"11402","title":"Graph planning with expected finite horizon","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"doi":"10.1016/j.jcss.2022.04.003","abstract":[{"text":"Fixed-horizon planning considers a weighted graph and asks to construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping-time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary as the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping-time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time.","lang":"eng"}],"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1802.03642"}],"intvolume":"       129","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"KrCh"}],"date_created":"2022-05-22T22:01:40Z","scopus_import":"1","external_id":{"isi":["000805002800001"],"arxiv":["1802.03642"]},"date_published":"2022-11-01T00:00:00Z","date_updated":"2025-07-14T09:09:54Z","publication":"Journal of Computer and System Sciences","page":"1-21","article_type":"original","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7402"}]},"oa":1,"year":"2022"},{"doi":"10.1093/genetics/iyac083","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"issue":"3","_id":"11411","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","author":[{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"orcid":"0000-0002-7354-8574","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina"},{"orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"}],"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","publication_status":"published","status":"public","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"publication_identifier":{"eissn":["1943-2631"]},"oa_version":"Submitted Version","file_date_updated":"2022-05-26T12:48:21Z","month":"07","ddc":["576"],"pmid":1,"citation":{"short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>."},"day":"01","volume":221,"article_processing_charge":"No","has_accepted_license":"1","file":[{"checksum":"cc2d56deb608bd53c5cc02f03a875107","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-05-26T12:48:15Z","success":1,"file_size":885374,"creator":"larathoo","relation":"main_file","file_name":"Manuscript.pdf","date_created":"2022-05-26T12:48:15Z","file_id":"11412"},{"file_id":"11413","date_created":"2022-05-26T12:48:21Z","file_name":"SupplementalMaterial.pdf","file_size":1401704,"relation":"main_file","creator":"larathoo","access_level":"open_access","content_type":"application/pdf","checksum":"693742595b6c7ed809423be01460d083","success":1,"date_updated":"2022-05-26T12:48:21Z"}],"year":"2022","oa":1,"article_number":"iyac083","article_type":"original","related_material":{"record":[{"id":"14651","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"11321"},{"id":"9192","status":"public","relation":"research_data"}]},"date_updated":"2024-02-21T12:38:33Z","publication":"Genetics","date_created":"2022-05-26T13:44:50Z","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","date_published":"2022-07-01T00:00:00Z","external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Oxford University Press","intvolume":"       221"},{"publication_status":"published","status":"public","acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","publication_identifier":{"issn":["0003-6951"]},"issue":"19","abstract":[{"lang":"eng","text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n"}],"doi":"10.1063/5.0097339","author":[{"first_name":"Anthony J.","full_name":"Sigillito, Anthony J.","last_name":"Sigillito"},{"first_name":"Jacob P.","full_name":"Covey, Jacob P.","last_name":"Covey"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Karl","full_name":"Petersson, Karl","last_name":"Petersson"},{"first_name":"Stefan","last_name":"Preble","full_name":"Preble, Stefan"}],"title":"Emerging qubit systems: Guest editorial","_id":"11417","volume":120,"article_processing_charge":"No","oa_version":"Published Version","day":"12","citation":{"short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401.","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>","ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022.","chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>.","mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>."},"month":"05","article_type":"letter_note","article_number":"190401","publication":"Applied Physics Letters","date_updated":"2023-08-03T07:16:20Z","year":"2022","oa":1,"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0097339"}],"intvolume":"       120","publisher":"American Institute of Physics","date_published":"2022-05-12T00:00:00Z","external_id":{"isi":["000796002100002"]},"scopus_import":"1","date_created":"2022-05-29T22:01:53Z","department":[{"_id":"JoFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-03T07:16:53Z","publication":"Annals of Probability","page":"984-1012","article_type":"original","oa":1,"year":"2022","publisher":"Institute of Mathematical Statistics","intvolume":"        50","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LaEr"}],"date_created":"2022-05-29T22:01:53Z","scopus_import":"1","date_published":"2022-05-01T00:00:00Z","external_id":{"arxiv":["2103.06730"],"isi":["000793963400005"]},"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"publication_status":"published","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","status":"public","_id":"11418","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","author":[{"orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","orcid":"0000-0002-2904-1856"}],"doi":"10.1214/21-AOP1552","abstract":[{"lang":"eng","text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048)."}],"issue":"3","arxiv":1,"article_processing_charge":"No","volume":50,"month":"05","citation":{"mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>"},"day":"01","oa_version":"Preprint"},{"article_type":"original","article_number":"e73542","date_updated":"2023-08-03T07:15:49Z","publication":"eLife","year":"2022","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":"        11","publisher":"eLife Sciences Publications","scopus_import":"1","date_created":"2022-05-29T22:01:54Z","external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"date_published":"2022-05-05T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"publication_status":"published","status":"public","acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/eLife.73542","abstract":[{"text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission.","lang":"eng"}],"_id":"11419","author":[{"first_name":"Tetsuya","last_name":"Hori","full_name":"Hori, Tetsuya"},{"first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546"},{"last_name":"Wang","full_name":"Wang, Han Ying","first_name":"Han Ying"},{"last_name":"Miyasaka","full_name":"Miyasaka, Tomohiro","first_name":"Tomohiro"},{"first_name":"Laurent","full_name":"Guillaud, Laurent","last_name":"Guillaud"},{"first_name":"Zacharie","last_name":"Taoufiq","full_name":"Taoufiq, Zacharie"},{"full_name":"Mahapatra, Satyajit","last_name":"Mahapatra","first_name":"Satyajit"},{"first_name":"Hiroshi","full_name":"Yamada, Hiroshi","last_name":"Yamada"},{"full_name":"Takei, Kohji","last_name":"Takei","first_name":"Kohji"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","volume":11,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11421","date_created":"2022-05-30T08:09:16Z","file_name":"elife-73542-v2.pdf","file_size":2466296,"creator":"cchlebak","relation":"main_file","access_level":"open_access","checksum":"ccddbd167e00ff8375f12998af497152","content_type":"application/pdf","success":1,"date_updated":"2022-05-30T08:09:16Z"}],"oa_version":"Published Version","file_date_updated":"2022-05-30T08:09:16Z","ddc":["616"],"month":"05","pmid":1,"day":"05","citation":{"mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>.","short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542.","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."}},{"oa":1,"year":"2022","date_updated":"2024-09-10T13:03:17Z","publication":"Journal of Machine Learning Research","page":"1-55","article_type":"original","related_material":{"link":[{"url":"https://www.jmlr.org/papers/v23/21-1365.html","relation":"other"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"date_created":"2022-05-29T22:01:54Z","scopus_import":"1","date_published":"2022-04-01T00:00:00Z","external_id":{"arxiv":["2111.02278"]},"publisher":"Journal of Machine Learning Research","intvolume":"        23","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"11420","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","author":[{"first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr"},{"full_name":"Kungurtsev, Vyacheslav","last_name":"Kungurtsev","first_name":"Vyacheslav"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"}],"abstract":[{"lang":"eng","text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory."}],"issue":"130","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","status":"public","publication_status":"published","month":"04","file_date_updated":"2022-05-30T08:22:55Z","ddc":["000"],"citation":{"mla":"Shevchenko, Aleksandr, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","chicago":"Shevchenko, Aleksandr, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research."},"day":"01","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"relation":"main_file","file_size":1521701,"creator":"cchlebak","file_name":"21-1365.pdf","date_updated":"2022-05-30T08:22:55Z","success":1,"content_type":"application/pdf","checksum":"d4ff5d1affb34848b5c5e4002483fc62","access_level":"open_access","date_created":"2022-05-30T08:22:55Z","file_id":"11422"}],"article_processing_charge":"No","volume":23,"has_accepted_license":"1"}]