[{"external_id":{"isi":["000766619100025"],"arxiv":["2007.11998"]},"author":[{"full_name":"Franceschini, Chiara","last_name":"Franceschini","first_name":"Chiara"},{"full_name":"Gonçalves, Patrícia","first_name":"Patrícia","last_name":"Gonçalves"},{"full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","last_name":"Sau","first_name":"Federico"}],"volume":28,"publication_identifier":{"issn":["1350-7265"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"_id":"12281","abstract":[{"text":"We study the hydrodynamic and hydrostatic limits of the one-dimensional open symmetric inclusion process with slow boundary. Depending on the value of the parameter tuning the interaction rate of the bulk of the system with the boundary, we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary conditions as hydrodynamic equation. In our approach, we combine duality and first-second class particle techniques to reduce the scaling limit of the inclusion process to the limiting behavior of a single, non-interacting, particle.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Bernoulli Society for Mathematical Statistics and Probability","page":"1340-1381","status":"public","date_created":"2023-01-16T10:03:04Z","department":[{"_id":"JaMa"}],"keyword":["Statistics and Probability"],"isi":1,"day":"01","arxiv":1,"oa":1,"issue":"2","quality_controlled":"1","ec_funded":1,"article_type":"original","doi":"10.3150/21-bej1390","oa_version":"Preprint","citation":{"short":"C. Franceschini, P. Gonçalves, F. Sau, Bernoulli 28 (2022) 1340–1381.","apa":"Franceschini, C., Gonçalves, P., &#38; Sau, F. (2022). Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/21-bej1390\">https://doi.org/10.3150/21-bej1390</a>","chicago":"Franceschini, Chiara, Patrícia Gonçalves, and Federico Sau. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2022. <a href=\"https://doi.org/10.3150/21-bej1390\">https://doi.org/10.3150/21-bej1390</a>.","ista":"Franceschini C, Gonçalves P, Sau F. 2022. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 28(2), 1340–1381.","ama":"Franceschini C, Gonçalves P, Sau F. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. <i>Bernoulli</i>. 2022;28(2):1340-1381. doi:<a href=\"https://doi.org/10.3150/21-bej1390\">10.3150/21-bej1390</a>","mla":"Franceschini, Chiara, et al. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” <i>Bernoulli</i>, vol. 28, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2022, pp. 1340–81, doi:<a href=\"https://doi.org/10.3150/21-bej1390\">10.3150/21-bej1390</a>.","ieee":"C. Franceschini, P. Gonçalves, and F. Sau, “Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics,” <i>Bernoulli</i>, vol. 28, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1340–1381, 2022."},"date_updated":"2023-08-04T10:27:35Z","type":"journal_article","scopus_import":"1","month":"05","date_published":"2022-05-01T00:00:00Z","article_processing_charge":"No","publication":"Bernoulli","language":[{"iso":"eng"}],"year":"2022","acknowledgement":"C.F. and P.G. thank FCT/Portugal for support through the project UID/MAT/04459/2013.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovative programme (grant agreement No. 715734). F.S. was founded by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.\r\nF.S. wishes to thank Joe P. Chen for some fruitful discussions at an early stage of this work. F.S. thanks CAMGSD, IST, Lisbon, where part of this work has been done, and the European research and innovative programme No. 715734 for the kind hospitality.","intvolume":"        28","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2007.11998","open_access":"1"}],"title":"Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics"},{"publisher":"The Company of Biologists","status":"public","date_created":"2023-01-16T10:03:14Z","isi":1,"day":"19","department":[{"_id":"SiHi"},{"_id":"LeSa"}],"quality_controlled":"1","issue":"8","external_id":{"pmid":["35438168"],"isi":["000798123600015"]},"author":[{"orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Stouffer","full_name":"Stouffer, Melissa A"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","last_name":"Vercellino","first_name":"Irene","full_name":"Vercellino, Irene"}],"volume":135,"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"abstract":[{"text":"From a simple thought to a multicellular movement","lang":"eng"}],"_id":"12282","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","article_processing_charge":"No","publication":"Journal of Cell Science","language":[{"iso":"eng"}],"year":"2022","acknowledgement":"The authors want to thank Professors Carrie Bernecky, Tom Henzinger, Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant contribution to the discussion that lead to this article.","intvolume":"       135","title":"Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole","article_type":"letter_note","doi":"10.1242/jcs.260017","oa_version":"None","date_updated":"2023-08-04T10:28:04Z","citation":{"ama":"Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. <i>Journal of Cell Science</i>. 2022;135(8). doi:<a href=\"https://doi.org/10.1242/jcs.260017\">10.1242/jcs.260017</a>","mla":"Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” <i>Journal of Cell Science</i>, vol. 135, no. 8, 260017, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.260017\">10.1242/jcs.260017</a>.","ieee":"N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole,” <i>Journal of Cell Science</i>, vol. 135, no. 8. The Company of Biologists, 2022.","short":"N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022).","apa":"Amberg, N., Stouffer, M. A., &#38; Vercellino, I. (2022). Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260017\">https://doi.org/10.1242/jcs.260017</a>","chicago":"Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” <i>Journal of Cell Science</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.260017\">https://doi.org/10.1242/jcs.260017</a>.","ista":"Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 135(8), 260017."},"type":"journal_article","pmid":1,"article_number":"260017","month":"04","date_published":"2022-04-19T00:00:00Z","scopus_import":"1"},{"title":"Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography","intvolume":"       135","acknowledgement":"J.A. was supported by a grant from the Medical Research Council (MRC), UK (MR/R000352/1) to C.A.M. Cryo-EM data were collected on equipment funded by the Wellcome Trust, UK (079605/Z/06/Z) and the Biotechnology and Biological Sciences Research Council (BBSRC) UK (BB/L014211/1). F.F.’s salary and institute were supported by Inserm (Institut National de la Santé et de la Recherche Médicale), CNRS (Centre National de la Recherche Scientifique) and Sorbonne Université. F.F.’s group was particularly supported by Agence Nationale de la\r\nRecherche (ANR-16-CE16-0011-03) and Seventh Framework Programme (EUHEALTH-\r\n2013, DESIRE, N° 60253; also funding M.S.’s salary) and the European Cooperation in Science and Technology (COST Action CA16118). Open Access funding provided by Birkbeck College: Birkbeck University of London. Deposited in PMC for immediate release.","year":"2022","language":[{"iso":"eng"}],"publication":"Journal of Cell Science","article_processing_charge":"No","ddc":["570"],"date_published":"2022-04-01T00:00:00Z","month":"04","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","pmid":1,"citation":{"ama":"Atherton J, Stouffer MA, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. 2022;135(7). doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>","mla":"Atherton, Joseph, et al. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>, vol. 135, no. 7, 259234, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>.","ieee":"J. Atherton, M. A. Stouffer, F. Francis, and C. A. Moores, “Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography,” <i>Journal of Cell Science</i>, vol. 135, no. 7. The Company of Biologists, 2022.","short":"J. Atherton, M.A. Stouffer, F. Francis, C.A. Moores, Journal of Cell Science 135 (2022).","apa":"Atherton, J., Stouffer, M. A., Francis, F., &#38; Moores, C. A. (2022). Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>","chicago":"Atherton, Joseph, Melissa A Stouffer, Fiona Francis, and Carolyn A. Moores. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>.","ista":"Atherton J, Stouffer MA, Francis F, Moores CA. 2022. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 135(7), 259234."},"date_updated":"2023-08-04T10:28:34Z","has_accepted_license":"1","article_number":"259234","oa_version":"Published Version","file_date_updated":"2023-01-30T11:41:01Z","article_type":"original","doi":"10.1242/jcs.259234","quality_controlled":"1","issue":"7","oa":1,"day":"01","isi":1,"keyword":["Cell Biology"],"department":[{"_id":"SiHi"}],"date_created":"2023-01-16T10:03:24Z","status":"public","file":[{"file_name":"2022_JourCellBiology_Atherton.pdf","access_level":"open_access","success":1,"checksum":"4346ed32cb7c89a8ca051c7da68a9a1c","date_created":"2023-01-30T11:41:01Z","file_size":13868733,"content_type":"application/pdf","date_updated":"2023-01-30T11:41:01Z","creator":"dernst","relation":"main_file","file_id":"12461"}],"publisher":"The Company of Biologists","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration."}],"_id":"12283","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"volume":135,"external_id":{"pmid":["35383828"],"isi":["000783840400010"]},"author":[{"last_name":"Atherton","first_name":"Joseph","full_name":"Atherton, Joseph"},{"last_name":"Stouffer","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","full_name":"Stouffer, Melissa A"},{"first_name":"Fiona","last_name":"Francis","full_name":"Francis, Fiona"},{"full_name":"Moores, Carolyn A.","first_name":"Carolyn A.","last_name":"Moores"}]},{"acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","title":"Loose cores and cycles in random hypergraphs","intvolume":"        29","article_processing_charge":"No","publication":"The Electronic Journal of Combinatorics","year":"2022","language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","date_updated":"2023-08-04T10:29:18Z","citation":{"ama":"Cooley O, Kang M, Zalla J. Loose cores and cycles in random hypergraphs. <i>The Electronic Journal of Combinatorics</i>. 2022;29(4). doi:<a href=\"https://doi.org/10.37236/10794\">10.37236/10794</a>","ieee":"O. Cooley, M. Kang, and J. Zalla, “Loose cores and cycles in random hypergraphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 29, no. 4. The Electronic Journal of Combinatorics, 2022.","mla":"Cooley, Oliver, et al. “Loose Cores and Cycles in Random Hypergraphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 29, no. 4, P4.13, The Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10794\">10.37236/10794</a>.","apa":"Cooley, O., Kang, M., &#38; Zalla, J. (2022). Loose cores and cycles in random hypergraphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10794\">https://doi.org/10.37236/10794</a>","short":"O. Cooley, M. Kang, J. Zalla, The Electronic Journal of Combinatorics 29 (2022).","ista":"Cooley O, Kang M, Zalla J. 2022. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 29(4), P4.13.","chicago":"Cooley, Oliver, Mihyun Kang, and Julian Zalla. “Loose Cores and Cycles in Random Hypergraphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10794\">https://doi.org/10.37236/10794</a>."},"license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"P4.13","ddc":["510"],"date_published":"2022-10-21T00:00:00Z","month":"10","scopus_import":"1","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"},"article_type":"original","doi":"10.37236/10794","oa_version":"Published Version","file_date_updated":"2023-01-30T11:45:13Z","day":"21","isi":1,"department":[{"_id":"MaKw"}],"keyword":["Computational Theory and Mathematics","Geometry and Topology","Theoretical Computer Science","Applied Mathematics","Discrete Mathematics and Combinatorics"],"quality_controlled":"1","oa":1,"issue":"4","file":[{"creator":"dernst","date_updated":"2023-01-30T11:45:13Z","content_type":"application/pdf","file_size":626953,"file_id":"12462","relation":"main_file","access_level":"open_access","file_name":"2022_ElecJournCombinatorics_Cooley_Kang_Zalla.pdf","date_created":"2023-01-30T11:45:13Z","checksum":"00122b2459f09b5ae43073bfba565e94","success":1}],"publisher":"The Electronic Journal of Combinatorics","date_created":"2023-01-16T10:03:57Z","status":"public","abstract":[{"text":"Inspired by the study of loose cycles in hypergraphs, we define the loose core in hypergraphs as a structurewhich mirrors the close relationship between cycles and $2$-cores in graphs. We prove that in the $r$-uniform binomial random hypergraph $H^r(n,p)$, the order of the loose core undergoes a phase transition at a certain critical threshold and determine this order, as well as the number of edges, asymptotically in the subcritical and supercritical regimes.&#x0D;\r\nOur main tool is an algorithm called CoreConstruct, which enables us to analyse a peeling process for the loose core. By analysing this algorithm we determine the asymptotic degree distribution of vertices in the loose core and in particular how many vertices and edges the loose core contains. As a corollary we obtain an improved upper bound on the length of the longest loose cycle in $H^r(n,p)$.","lang":"eng"}],"_id":"12286","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000876763300001"]},"author":[{"first_name":"Oliver","last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","full_name":"Cooley, Oliver"},{"full_name":"Kang, Mihyun","first_name":"Mihyun","last_name":"Kang"},{"full_name":"Zalla, Julian","last_name":"Zalla","first_name":"Julian"}],"publication_identifier":{"eissn":["1077-8926"]},"volume":29},{"acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","intvolume":"        11","publication":"eLife","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"year":"2022","type":"journal_article","pmid":1,"date_updated":"2023-08-04T10:29:48Z","has_accepted_license":"1","citation":{"ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>"},"article_number":"79848","ddc":["570"],"month":"09","date_published":"2022-09-15T00:00:00Z","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","doi":"10.7554/elife.79848","ec_funded":1,"oa_version":"Published Version","file_date_updated":"2023-01-30T11:50:53Z","day":"15","isi":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"department":[{"_id":"MaJö"},{"_id":"PeJo"}],"quality_controlled":"1","oa":1,"file":[{"content_type":"application/pdf","file_size":8506811,"date_updated":"2023-01-30T11:50:53Z","creator":"dernst","file_id":"12463","relation":"main_file","access_level":"open_access","file_name":"2022_eLife_Sumser.pdf","success":1,"date_created":"2023-01-30T11:50:53Z","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b"}],"publisher":"eLife Sciences Publications","date_created":"2023-01-16T10:04:15Z","status":"public","abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"_id":"12288","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000892204300001"],"pmid":["36040301"]},"author":[{"last_name":"Sumser","orcid":"0000-0002-4792-1881","first_name":"Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","full_name":"Sumser, Anton L"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoav","last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","full_name":"Ben Simon, Yoav"}],"project":[{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"publication_identifier":{"eissn":["2050-084X"]},"volume":11},{"oa_version":"Published Version","file_date_updated":"2023-01-30T11:59:21Z","doi":"10.1214/22-ejp838","article_type":"original","ec_funded":1,"date_published":"2022-09-12T00:00:00Z","month":"09","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal multi-resolvent local laws for Wigner matrices. <i>Electronic Journal of Probability</i>. 2022;27:1-38. doi:<a href=\"https://doi.org/10.1214/22-ejp838\">10.1214/22-ejp838</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal multi-resolvent local laws for Wigner matrices,” <i>Electronic Journal of Probability</i>, vol. 27. Institute of Mathematical Statistics, pp. 1–38, 2022.","mla":"Cipolloni, Giorgio, et al. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” <i>Electronic Journal of Probability</i>, vol. 27, Institute of Mathematical Statistics, 2022, pp. 1–38, doi:<a href=\"https://doi.org/10.1214/22-ejp838\">10.1214/22-ejp838</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Optimal multi-resolvent local laws for Wigner matrices. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-ejp838\">https://doi.org/10.1214/22-ejp838</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 27 (2022) 1–38.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Optimal multi-resolvent local laws for Wigner matrices. Electronic Journal of Probability. 27, 1–38.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/22-ejp838\">https://doi.org/10.1214/22-ejp838</a>."},"has_accepted_license":"1","date_updated":"2023-08-04T10:32:23Z","type":"journal_article","year":"2022","language":[{"iso":"eng"}],"publication":"Electronic Journal of Probability","article_processing_charge":"No","intvolume":"        27","title":"Optimal multi-resolvent local laws for Wigner matrices","acknowledgement":"L. Erdős was supported by ERC Advanced Grant “RMTBeyond” No. 101020331. D. Schröder was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","project":[{"call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"volume":27,"publication_identifier":{"eissn":["1083-6489"]},"external_id":{"isi":["000910863700003"]},"author":[{"full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","orcid":"0000-0002-2904-1856","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"lang":"eng","text":"We prove local laws, i.e. optimal concentration estimates for arbitrary products of resolvents of a Wigner random matrix with deterministic matrices in between. We find that the size of such products heavily depends on whether some of the deterministic matrices are traceless. Our estimates correctly account for this dependence and they hold optimally down to the smallest possible spectral scale."}],"_id":"12290","status":"public","date_created":"2023-01-16T10:04:38Z","page":"1-38","publisher":"Institute of Mathematical Statistics","file":[{"relation":"main_file","file_id":"12464","file_size":502149,"content_type":"application/pdf","date_updated":"2023-01-30T11:59:21Z","creator":"dernst","success":1,"checksum":"bb647b48fbdb59361210e425c220cdcb","date_created":"2023-01-30T11:59:21Z","file_name":"2022_ElecJournProbability_Cipolloni.pdf","access_level":"open_access"}],"quality_controlled":"1","oa":1,"isi":1,"day":"12","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"department":[{"_id":"LaEr"}]},{"file_date_updated":"2023-11-02T17:12:37Z","oa_version":"Submitted Version","ec_funded":1,"doi":"10.1038/s41586-022-05187-x","article_type":"original","scopus_import":"1","ddc":["580"],"date_published":"2022-09-15T00:00:00Z","month":"09","pmid":1,"type":"journal_article","citation":{"chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>"},"has_accepted_license":"1","date_updated":"2023-11-07T08:16:09Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"year":"2022","publication":"Nature","article_processing_charge":"No","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","intvolume":"       609","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"volume":609,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"last_name":"Fiedler","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","first_name":"Caterina","full_name":"Giannini, Caterina"},{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","first_name":"Marek"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"}],"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12291","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"date_created":"2023-01-16T10:04:48Z","status":"public","file":[{"access_level":"open_access","file_name":"Friml Nature 2022_merged.pdf","date_created":"2023-11-02T17:12:37Z","checksum":"a6055c606aefb900bf62ae3e7d15f921","success":1,"date_updated":"2023-11-02T17:12:37Z","creator":"amally","content_type":"application/pdf","file_size":79774945,"file_id":"14483","relation":"main_file"}],"page":"575-581","publisher":"Springer Nature","oa":1,"issue":"7927","quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"day":"15","isi":1},{"oa_version":"Preprint","doi":"10.1007/978-3-031-18283-9_14","conference":{"location":"Radisson Grenada Beach Resort, Grenada","end_date":"2022-05-06","start_date":"2022-05-02","name":"FC: Financial Cryptography"},"alternative_title":["LNCS"],"scopus_import":"1","month":"10","date_published":"2022-10-22T00:00:00Z","type":"conference","citation":{"ieee":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, and Z. Xiang, “Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback,” in <i>Financial Cryptography and Data Security</i>, Radisson Grenada Beach Resort, Grenada, 2022, vol. 13411, pp. 296–315.","mla":"Gelashvili, Rati, et al. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” <i>Financial Cryptography and Data Security</i>, vol. 13411, Springer Nature, 2022, pp. 296–315, doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">10.1007/978-3-031-18283-9_14</a>.","ama":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In: <i>Financial Cryptography and Data Security</i>. Vol 13411. Springer Nature; 2022:296-315. doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">10.1007/978-3-031-18283-9_14</a>","ista":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. 2022. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 13411, 296–315.","chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alberto Sonnino, Alexander Spiegelman, and Zhuolun Xiang. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” In <i>Financial Cryptography and Data Security</i>, 13411:296–315. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">https://doi.org/10.1007/978-3-031-18283-9_14</a>.","apa":"Gelashvili, R., Kokoris Kogias, E., Sonnino, A., Spiegelman, A., &#38; Xiang, Z. (2022). Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In <i>Financial Cryptography and Data Security</i> (Vol. 13411, pp. 296–315). Radisson Grenada Beach Resort, Grenada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">https://doi.org/10.1007/978-3-031-18283-9_14</a>","short":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, Z. Xiang, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 296–315."},"date_updated":"2023-09-05T15:13:17Z","language":[{"iso":"eng"}],"year":"2022","article_processing_charge":"No","publication":"Financial Cryptography and Data Security","title":"Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2106.10362","open_access":"1"}],"intvolume":"     13411","acknowledgement":"We thank our shepherd Aniket Kate and the anonymous reviewers at FC 2022 for their helpful feedback. This work is supported by the Novi team at Facebook. We also thank the Novi Research and Engineering teams for valuable feedback, and in particular Mathieu Baudet, Andrey Chursin, George Danezis, Zekun Li, and Dahlia Malkhi for discussions that shaped this work.","publication_identifier":{"isbn":["9783031182822"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783031182839"]},"volume":13411,"author":[{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"},{"last_name":"Xiang","first_name":"Zhuolun","full_name":"Xiang, Zhuolun"}],"external_id":{"arxiv":["2106.10362"]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12298","abstract":[{"lang":"eng","text":"Existing committee-based Byzantine state machine replication (SMR) protocols, typically deployed in production blockchains, face a clear trade-off: (1) they either achieve linear communication cost in the steady state, but sacrifice liveness during periods of asynchrony, or (2) they are robust (progress with probability one) but pay quadratic communication cost. We believe this trade-off is unwarranted since existing linear protocols still have asymptotic quadratic cost in the worst case. We design Ditto, a Byzantine SMR protocol that enjoys the best of both worlds: optimal communication on and off the steady state (linear and quadratic, respectively) and progress guarantee under asynchrony and DDoS attacks. We achieve this by replacing the view-synchronization of partially synchronous protocols with an asynchronous fallback mechanism at no extra asymptotic cost. Specifically, we start from HotStuff, a state-of-the-art linear protocol, and gradually build Ditto. As a separate contribution and an intermediate step, we design a 2-chain version of HotStuff, Jolteon, which leverages a quadratic view-change mechanism to reduce the latency of the standard 3-chain HotStuff. We implement and experimentally evaluate all our systems to prove that breaking the robustness-efficiency trade-off is in the realm of practicality."}],"date_created":"2023-01-16T10:05:51Z","status":"public","page":"296-315","publisher":"Springer Nature","oa":1,"arxiv":1,"quality_controlled":"1","department":[{"_id":"ElKo"}],"day":"22"},{"title":"How well do sparse ImageNet models transfer?","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.13445","open_access":"1"}],"acknowledgement":"he authors would like to sincerely thank Christoph Lampert and Nir Shavit for fruitful discussions during the development of this work, and Eldar Kurtic for experimental support. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35, while AP and DA acknowledge generous support by the ERC, via Starting Grant 805223 ScaleML.","language":[{"iso":"eng"}],"year":"2022","article_processing_charge":"No","publication":"2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition","scopus_import":"1","date_published":"2022-09-27T00:00:00Z","month":"09","type":"conference","citation":{"ama":"Iofinova EB, Peste E-A, Kurtz M, Alistarh D-A. How well do sparse ImageNet models transfer? In: <i>2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Institute of Electrical and Electronics Engineers; 2022:12256-12266. doi:<a href=\"https://doi.org/10.1109/cvpr52688.2022.01195\">10.1109/cvpr52688.2022.01195</a>","ieee":"E. B. Iofinova, E.-A. Peste, M. Kurtz, and D.-A. Alistarh, “How well do sparse ImageNet models transfer?,” in <i>2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, New Orleans, LA, United States, 2022, pp. 12256–12266.","mla":"Iofinova, Eugenia B., et al. “How Well Do Sparse ImageNet Models Transfer?” <i>2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Institute of Electrical and Electronics Engineers, 2022, pp. 12256–66, doi:<a href=\"https://doi.org/10.1109/cvpr52688.2022.01195\">10.1109/cvpr52688.2022.01195</a>.","apa":"Iofinova, E. B., Peste, E.-A., Kurtz, M., &#38; Alistarh, D.-A. (2022). How well do sparse ImageNet models transfer? In <i>2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 12256–12266). New Orleans, LA, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/cvpr52688.2022.01195\">https://doi.org/10.1109/cvpr52688.2022.01195</a>","short":"E.B. Iofinova, E.-A. Peste, M. Kurtz, D.-A. Alistarh, in:, 2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Institute of Electrical and Electronics Engineers, 2022, pp. 12256–12266.","ista":"Iofinova EB, Peste E-A, Kurtz M, Alistarh D-A. 2022. How well do sparse ImageNet models transfer? 2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Computer Vision and Pattern Recognition, 12256–12266.","chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, Mark Kurtz, and Dan-Adrian Alistarh. “How Well Do Sparse ImageNet Models Transfer?” In <i>2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 12256–66. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/cvpr52688.2022.01195\">https://doi.org/10.1109/cvpr52688.2022.01195</a>."},"date_updated":"2023-08-04T10:33:28Z","oa_version":"Preprint","ec_funded":1,"doi":"10.1109/cvpr52688.2022.01195","conference":{"end_date":"2022-06-24","start_date":"2022-06-18","name":"CVPR: Computer Vision and Pattern Recognition","location":"New Orleans, LA, United States"},"related_material":{"record":[{"status":"public","id":"13074","relation":"dissertation_contains"}]},"oa":1,"arxiv":1,"quality_controlled":"1","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"day":"27","isi":1,"date_created":"2023-01-16T10:06:00Z","status":"public","page":"12256-12266","publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12299","abstract":[{"lang":"eng","text":"Transfer learning is a classic paradigm by which models pretrained on large “upstream” datasets are adapted to yield good results on “downstream” specialized datasets. Generally, more accurate models on the “upstream” dataset tend to provide better transfer accuracy “downstream”. In this work, we perform an in-depth investigation of this phenomenon in the context of convolutional neural networks (CNNs) trained on the ImageNet dataset, which have been pruned-that is, compressed by sparsifiying their connections. We consider transfer using unstructured pruned models obtained by applying several state-of-the-art pruning methods, including magnitude-based, second-order, regrowth, lottery-ticket, and regularization approaches, in the context of twelve standard transfer tasks. In a nutshell, our study shows that sparse models can match or even outperform the transfer performance of dense models, even at high sparsities, and, while doing so, can lead to significant inference and even training speedups. At the same time, we observe and analyze significant differences in the behaviour of different pruning methods. The code is available at: https://github.com/IST-DASLab/sparse-imagenet-transfer."}],"publication_identifier":{"eissn":["2575-7075"]},"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":" W1260-N35"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"}],"author":[{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","orcid":"0000-0002-7778-3221","first_name":"Eugenia B","full_name":"Iofinova, Eugenia B"},{"full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","last_name":"Peste"},{"first_name":"Mark","last_name":"Kurtz","full_name":"Kurtz, Mark"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"external_id":{"arxiv":["2111.13445"],"isi":["000870759105034"]}},{"scopus_import":"1","publication_status":"published","date_published":"2022-07-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","_id":"12300","type":"conference","abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted third party and is a building block to decentralized protocols such as randomness beacons, threshold signatures, and general multiparty computation. Until recently, DKG protocols have assumed the synchronous model and thus are vulnerable when their underlying network assumptions do not hold. The recent advancements in asynchronous DKG protocols are insufficient as they either have poor efficiency or limited functionality, resulting in a lack of concrete implementations. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol. In a network of n nodes, our ADKG protocol can tolerate up to t<n/3 malicious nodes and have an expected O(κn3) communication cost, where κ is the security parameter. Our ADKG protocol produces a field element as the secret and is thus compatible with off-the-shelf threshold cryptosystems. We implement our ADKG protocol and evaluate it using a network of up to 128 nodes in geographically distributed AWS instances. Our evaluation shows that our protocol takes as low as 3 and 9.5 seconds to terminate for 32 and 64 nodes, respectively. Also, each node sends only 0.7 Megabytes and 2.9 Megabytes of data during the two experiments, respectively.","lang":"eng"}],"citation":{"chicago":"Das, Sourav, Thomas Yurek, Zhuolun Xiang, Andrew Miller, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous Distributed Key Generation.” In <i>2022 IEEE Symposium on Security and Privacy</i>, 2518–34. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">https://doi.org/10.1109/sp46214.2022.9833584</a>.","ista":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. 2022. Practical asynchronous distributed key generation. 2022 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 2518–2534.","short":"S. Das, T. Yurek, Z. Xiang, A. Miller, E. Kokoris Kogias, L. Ren, in:, 2022 IEEE Symposium on Security and Privacy, Institute of Electrical and Electronics Engineers, 2022, pp. 2518–2534.","apa":"Das, S., Yurek, T., Xiang, Z., Miller, A., Kokoris Kogias, E., &#38; Ren, L. (2022). Practical asynchronous distributed key generation. In <i>2022 IEEE Symposium on Security and Privacy</i> (pp. 2518–2534). San Francisco, CA, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">https://doi.org/10.1109/sp46214.2022.9833584</a>","mla":"Das, Sourav, et al. “Practical Asynchronous Distributed Key Generation.” <i>2022 IEEE Symposium on Security and Privacy</i>, Institute of Electrical and Electronics Engineers, 2022, pp. 2518–34, doi:<a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">10.1109/sp46214.2022.9833584</a>.","ieee":"S. Das, T. Yurek, Z. Xiang, A. Miller, E. Kokoris Kogias, and L. Ren, “Practical asynchronous distributed key generation,” in <i>2022 IEEE Symposium on Security and Privacy</i>, San Francisco, CA, United States, 2022, pp. 2518–2534.","ama":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. Practical asynchronous distributed key generation. In: <i>2022 IEEE Symposium on Security and Privacy</i>. Institute of Electrical and Electronics Engineers; 2022:2518-2534. doi:<a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">10.1109/sp46214.2022.9833584</a>"},"date_updated":"2023-02-16T07:43:53Z","publication_identifier":{"eissn":["2375-1207"],"eisbn":["9781665413169"]},"oa_version":"Preprint","conference":{"end_date":"2022-05-26","name":"SP: Symposium on Security and Privacy","start_date":"2022-05-23","location":"San Francisco, CA, United States"},"doi":"10.1109/sp46214.2022.9833584","author":[{"last_name":"Das","first_name":"Sourav","full_name":"Das, Sourav"},{"last_name":"Yurek","first_name":"Thomas","full_name":"Yurek, Thomas"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"},{"full_name":"Miller, Andrew","first_name":"Andrew","last_name":"Miller"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Ren, Ling","last_name":"Ren","first_name":"Ling"}],"oa":1,"quality_controlled":"1","title":"Practical asynchronous distributed key generation","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1591"}],"department":[{"_id":"ElKo"}],"acknowledgement":"The authors would like to thank Amit Agarwal, Adithya Bhat, Kobi Gurkan, Dakshita Khurana, Nibesh Shrestha, and Gilad Stern for the helpful discussions related to the paper.\r\nAlso, the authors would like to thank Sylvain Bellemare for helping with the hbACSS codebase and Nicolas Gailly for helping with running the Drand experiments.","day":"27","language":[{"iso":"eng"}],"year":"2022","date_created":"2023-01-16T10:06:11Z","status":"public","publication":"2022 IEEE Symposium on Security and Privacy","article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers","page":"2518-2534"},{"acknowledgement":"This work was partially funded by the ESF Investing in your future, the Madrid regional project S2018/TCS-4339 BLOQUES, the Spanish project PGC2018-102210-B-I00 BOSCO, the Ramón y Cajal fellowship RYC-2016-20281, and the ERC grant PR1001ERC02.","title":"FORQ-based language inclusion formal testing","intvolume":"     13372","publication":"Computer Aided Verification","article_processing_charge":"No","year":"2022","language":[{"iso":"eng"}],"type":"conference","has_accepted_license":"1","date_updated":"2023-09-05T15:13:36Z","citation":{"chicago":"Doveri, Kyveli, Pierre Ganty, and Nicolas Adrien Mazzocchi. “FORQ-Based Language Inclusion Formal Testing.” In <i>Computer Aided Verification</i>, 13372:109–29. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>.","ista":"Doveri K, Ganty P, Mazzocchi NA. 2022. FORQ-based language inclusion formal testing. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13372, 109–129.","short":"K. Doveri, P. Ganty, N.A. Mazzocchi, in:, Computer Aided Verification, Springer Nature, 2022, pp. 109–129.","apa":"Doveri, K., Ganty, P., &#38; Mazzocchi, N. A. (2022). FORQ-based language inclusion formal testing. In <i>Computer Aided Verification</i> (Vol. 13372, pp. 109–129). Haifa, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>","mla":"Doveri, Kyveli, et al. “FORQ-Based Language Inclusion Formal Testing.” <i>Computer Aided Verification</i>, vol. 13372, Springer Nature, 2022, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>.","ieee":"K. Doveri, P. Ganty, and N. A. Mazzocchi, “FORQ-based language inclusion formal testing,” in <i>Computer Aided Verification</i>, Haifa, Israel, 2022, vol. 13372, pp. 109–129.","ama":"Doveri K, Ganty P, Mazzocchi NA. FORQ-based language inclusion formal testing. In: <i>Computer Aided Verification</i>. Vol 13372. Springer Nature; 2022:109-129. doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>"},"ddc":["000"],"date_published":"2022-08-06T00:00:00Z","month":"08","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"location":"Haifa, Israel","name":"CAV: Computer Aided Verification","start_date":"2022-08-07","end_date":"2022-08-10"},"doi":"10.1007/978-3-031-13188-2_6","alternative_title":["LNCS"],"ec_funded":1,"oa_version":"Published Version","file_date_updated":"2023-01-30T12:51:02Z","day":"06","isi":1,"department":[{"_id":"ToHe"}],"quality_controlled":"1","oa":1,"arxiv":1,"page":"109-129","file":[{"file_id":"12465","relation":"main_file","content_type":"application/pdf","file_size":497682,"date_updated":"2023-01-30T12:51:02Z","creator":"dernst","success":1,"date_created":"2023-01-30T12:51:02Z","checksum":"edc363b1be5447a09063e115c247918a","access_level":"open_access","file_name":"2022_LNCS_Doveri.pdf"}],"publisher":"Springer Nature","date_created":"2023-01-16T10:06:31Z","status":"public","abstract":[{"text":"We propose a novel algorithm to decide the language inclusion between (nondeterministic) Büchi automata, a PSPACE-complete problem. Our approach, like others before, leverage a notion of quasiorder to prune the search for a counterexample by discarding candidates which are subsumed by others for the quasiorder. Discarded candidates are guaranteed to not compromise the completeness of the algorithm. The novelty of our work lies in the quasiorder used to discard candidates. We introduce FORQs (family of right quasiorders) that we obtain by adapting the notion of family of right congruences put forward by Maler and Staiger in 1993. We define a FORQ-based inclusion algorithm which we prove correct and instantiate it for a specific FORQ, called the structural FORQ, induced by the Büchi automaton to the right of the inclusion sign. The resulting implementation, called FORKLIFT, scales up better than the state-of-the-art on a variety of benchmarks including benchmarks from program verification and theorem proving for word combinatorics. Artifact: https://doi.org/10.5281/zenodo.6552870","lang":"eng"}],"_id":"12302","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000870310500006"],"arxiv":["2207.13549"]},"author":[{"last_name":"Doveri","first_name":"Kyveli","full_name":"Doveri, Kyveli"},{"first_name":"Pierre","last_name":"Ganty","full_name":"Ganty, Pierre"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publication_identifier":{"isbn":["9783031131875"],"eissn":["1611-3349"],"eisbn":["9783031131882"],"issn":["0302-9743"]},"volume":13372},{"acknowledgement":"I.M. thanks Zhijie Dong for long-term discussions on the material that entered this work. We thank Misha Finkelberg for pointing out errors in earlier versions. His advice and his insistence have led to a much better paper. A part of the writing was done at the conference at IST (Vienna) attended by all coauthors. We therefore thank the organizers of the conference and the support of ERC Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593. The work of I.M. was partially supported by NSF grants. The work of Y.Y. was partially supported by the Australian Research Council (ARC) via the award DE190101231. The work of G.Z. was partially supported by ARC via the award DE190101222.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1810.10095"}],"title":"Loop Grassmannians of Quivers and Affine Quantum Groups","article_processing_charge":"No","publication":"Representation Theory and Algebraic Geometry","language":[{"iso":"eng"}],"year":"2022","citation":{"ista":"Mirković I, Yang Y, Zhao G. 2022.Loop Grassmannians of Quivers and Affine Quantum Groups. In: Representation Theory and Algebraic Geometry. Trends in Mathematics, , 347–392.","chicago":"Mirković, Ivan, Yaping Yang, and Gufang Zhao. “Loop Grassmannians of Quivers and Affine Quantum Groups.” In <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky, Nicolas Guay, and Travis Schedler, 1st ed., 347–92. TM. Cham: Springer Nature; Birkhäuser, 2022. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>.","apa":"Mirković, I., Yang, Y., &#38; Zhao, G. (2022). Loop Grassmannians of Quivers and Affine Quantum Groups. In V. Baranovskky, N. Guay, &#38; T. Schedler (Eds.), <i>Representation Theory and Algebraic Geometry</i> (1st ed., pp. 347–392). Cham: Springer Nature; Birkhäuser. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>","short":"I. Mirković, Y. Yang, G. Zhao, in:, V. Baranovskky, N. Guay, T. Schedler (Eds.), Representation Theory and Algebraic Geometry, 1st ed., Springer Nature; Birkhäuser, Cham, 2022, pp. 347–392.","ieee":"I. Mirković, Y. Yang, and G. Zhao, “Loop Grassmannians of Quivers and Affine Quantum Groups,” in <i>Representation Theory and Algebraic Geometry</i>, 1st ed., V. Baranovskky, N. Guay, and T. Schedler, Eds. Cham: Springer Nature; Birkhäuser, 2022, pp. 347–392.","mla":"Mirković, Ivan, et al. “Loop Grassmannians of Quivers and Affine Quantum Groups.” <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky et al., 1st ed., Springer Nature; Birkhäuser, 2022, pp. 347–92, doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>.","ama":"Mirković I, Yang Y, Zhao G. Loop Grassmannians of Quivers and Affine Quantum Groups. In: Baranovskky V, Guay N, Schedler T, eds. <i>Representation Theory and Algebraic Geometry</i>. 1st ed. TM. Cham: Springer Nature; Birkhäuser; 2022:347-392. doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>"},"date_updated":"2023-01-27T07:07:31Z","type":"book_chapter","scopus_import":"1","month":"06","date_published":"2022-06-16T00:00:00Z","ec_funded":1,"alternative_title":["Trends in Mathematics"],"doi":"10.1007/978-3-030-82007-7_8","editor":[{"full_name":"Baranovskky, Vladimir","last_name":"Baranovskky","first_name":"Vladimir"},{"first_name":"Nicolas","last_name":"Guay","full_name":"Guay, Nicolas"},{"full_name":"Schedler, Travis","last_name":"Schedler","first_name":"Travis"}],"oa_version":"Preprint","department":[{"_id":"TaHa"}],"series_title":"TM","day":"16","arxiv":1,"oa":1,"quality_controlled":"1","page":"347-392","publisher":"Springer Nature; Birkhäuser","status":"public","date_created":"2023-01-16T10:06:41Z","_id":"12303","edition":"1","abstract":[{"text":"We construct for each choice of a quiver Q, a cohomology theory A, and a poset P a “loop Grassmannian” GP(Q,A). This generalizes loop Grassmannians of semisimple groups and the loop Grassmannians of based quadratic forms. The addition of a “dilation” torus D⊆G2m gives a quantization GPD(Q,A). This construction is motivated by the program of introducing an inner cohomology theory in algebraic geometry adequate for the Geometric Langlands program (Mirković, Some extensions of the notion of loop Grassmannians. Rad Hrvat. Akad. Znan. Umjet. Mat. Znan., the Mardešić issue. No. 532, 53–74, 2017) and on the construction of affine quantum groups from generalized cohomology theories (Yang and Zhao, Quiver varieties and elliptic quantum groups, preprint. arxiv1708.01418).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"arxiv":["1810.10095"]},"author":[{"full_name":"Mirković, Ivan","first_name":"Ivan","last_name":"Mirković"},{"last_name":"Yang","first_name":"Yaping","full_name":"Yang, Yaping"},{"full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","last_name":"Zhao"}],"place":"Cham","publication_identifier":{"eissn":["2297-024X"],"isbn":["9783030820060"],"issn":["2297-0215"],"eisbn":["9783030820077"]},"project":[{"call_identifier":"FP7","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces"}]},{"page":"1394-1434","publisher":"Taylor & Francis","status":"public","date_created":"2023-01-16T10:06:50Z","department":[{"_id":"JuFi"}],"keyword":["Applied Mathematics","Analysis"],"isi":1,"day":"01","arxiv":1,"oa":1,"issue":"7","quality_controlled":"1","author":[{"last_name":"De Nitti","first_name":"Nicola","full_name":"De Nitti, Nicola"},{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L"}],"external_id":{"arxiv":["1907.05342"],"isi":["000805689800001"]},"volume":47,"publication_identifier":{"issn":["0360-5302"],"eissn":["1532-4133"]},"_id":"12304","abstract":[{"lang":"eng","text":"We establish sharp criteria for the instantaneous propagation of free boundaries in solutions to the thin-film equation. The criteria are formulated in terms of the initial distribution of mass (as opposed to previous almost-optimal results), reflecting the fact that mass is a locally conserved quantity for the thin-film equation. In the regime of weak slippage, our criteria are at the same time necessary and sufficient. The proof of our upper bounds on free boundary propagation is based on a strategy of “propagation of degeneracy” down to arbitrarily small spatial scales: We combine estimates on the local mass and estimates on energies to show that “degeneracy” on a certain space-time cylinder entails “degeneracy” on a spatially smaller space-time cylinder with the same time horizon. The derivation of our lower bounds on free boundary propagation is based on a combination of a monotone quantity and almost optimal estimates established previously by the second author with a new estimate connecting motion of mass to entropy production."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","article_processing_charge":"No","publication":"Communications in Partial Differential Equations","year":"2022","language":[{"iso":"eng"}],"acknowledgement":"N. De Nitti acknowledges the kind hospitality of IST Austria within the framework of the ISTernship Summer Program 2018, during which most of the present article was written. N. DeNitti has received funding by The Austrian Agency for International Cooperation in Education &Research (OeAD-GmbH) via its financial support of the ISTernship Summer Program 2018. N.De Nitti would also like to thank Giuseppe Coclite, Giuseppe Devillanova, Giuseppe Florio, Sebastian Hensel, and Francesco Maddalena for several helpful conversations on topics related to this work.","intvolume":"        47","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1907.05342","open_access":"1"}],"title":"Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation","article_type":"original","doi":"10.1080/03605302.2022.2056702","oa_version":"Preprint","date_updated":"2023-08-04T10:34:31Z","citation":{"mla":"De Nitti, Nicola, and Julian L. Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7, Taylor &#38; Francis, 2022, pp. 1394–434, doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>.","ieee":"N. De Nitti and J. L. Fischer, “Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation,” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7. Taylor &#38; Francis, pp. 1394–1434, 2022.","ama":"De Nitti N, Fischer JL. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. 2022;47(7):1394-1434. doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>","chicago":"De Nitti, Nicola, and Julian L Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>.","ista":"De Nitti N, Fischer JL. 2022. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. Communications in Partial Differential Equations. 47(7), 1394–1434.","short":"N. De Nitti, J.L. Fischer, Communications in Partial Differential Equations 47 (2022) 1394–1434.","apa":"De Nitti, N., &#38; Fischer, J. L. (2022). Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>"},"type":"journal_article","scopus_import":"1","month":"07","date_published":"2022-07-01T00:00:00Z"},{"citation":{"short":"H. Abels, M. Moser, SIAM Journal on Mathematical Analysis 54 (2022) 114–172.","apa":"Abels, H., &#38; Moser, M. (2022). Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>","chicago":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>.","ista":"Abels H, Moser M. 2022. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. SIAM Journal on Mathematical Analysis. 54(1), 114–172.","ama":"Abels H, Moser M. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):114-172. doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>","mla":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 114–72, doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>.","ieee":"H. Abels and M. Moser, “Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 114–172, 2022."},"date_updated":"2023-08-04T10:34:56Z","type":"journal_article","date_published":"2022-01-04T00:00:00Z","month":"01","scopus_import":"1","doi":"10.1137/21m1424925","article_type":"original","oa_version":"Preprint","intvolume":"        54","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.08434","open_access":"1"}],"title":"Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°","publication":"SIAM Journal on Mathematical Analysis","article_processing_charge":"No","year":"2022","language":[{"iso":"eng"}],"abstract":[{"text":"This paper is concerned with the sharp interface limit for the Allen--Cahn equation with a nonlinear Robin boundary condition in a bounded smooth domain Ω⊂\\R2. We assume that a diffuse interface already has developed and that it is in contact with the boundary ∂Ω. The boundary condition is designed in such a way that the limit problem is given by the mean curvature flow with constant α-contact angle. For α close to 90° we prove a local in time convergence result for well-prepared initial data for times when a smooth solution to the limit problem exists. Based on the latter we construct a suitable curvilinear coordinate system and carry out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear Robin boundary condition. Moreover, we show a spectral estimate for the corresponding linearized Allen--Cahn operator and with its aid we derive strong norm estimates for the difference of the exact and approximate solutions using a Gronwall-type argument.","lang":"eng"}],"_id":"12305","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","external_id":{"arxiv":["2105.08434"],"isi":["000762768000004"]},"author":[{"full_name":"Abels, Helmut","first_name":"Helmut","last_name":"Abels"},{"first_name":"Maximilian","last_name":"Moser","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","full_name":"Moser, Maximilian"}],"volume":54,"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"isi":1,"day":"04","department":[{"_id":"JuFi"}],"keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"quality_controlled":"1","arxiv":1,"issue":"1","oa":1,"page":"114-172","publisher":"Society for Industrial and Applied Mathematics","status":"public","date_created":"2023-01-16T10:07:00Z"},{"title":"Tangible topology through the lens of limits","intvolume":"        32","year":"2022","language":[{"iso":"eng"}],"publication":"PRIMUS","article_processing_charge":"No","scopus_import":"1","month":"05","date_published":"2022-05-28T00:00:00Z","type":"journal_article","date_updated":"2023-01-30T13:02:30Z","citation":{"ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. <i>PRIMUS</i>. 2022;32(5):593-609. doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>","mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>, vol. 32, no. 5, Taylor &#38; Francis, 2022, pp. 593–609, doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>.","ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” <i>PRIMUS</i>, vol. 32, no. 5. Taylor &#38; Francis, pp. 593–609, 2022.","short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609.","apa":"Shipman, B. A., &#38; Stephenson, E. R. (2022). Tangible topology through the lens of limits. <i>PRIMUS</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>.","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609."},"oa_version":"None","article_type":"original","doi":"10.1080/10511970.2021.1872750","issue":"5","quality_controlled":"1","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"keyword":["Education","General Mathematics"],"day":"28","date_created":"2023-01-16T10:07:21Z","status":"public","page":"593-609","publisher":"Taylor & Francis","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12307","abstract":[{"lang":"eng","text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences."}],"publication_identifier":{"eissn":["1935-4053"],"issn":["1051-1970"]},"volume":32,"author":[{"last_name":"Shipman","first_name":"Barbara A.","full_name":"Shipman, Barbara A."},{"full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R","orcid":"0000-0002-6862-208X","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","date_published":"2022-12-21T00:00:00Z","month":"12","ddc":["570"],"has_accepted_license":"1","citation":{"mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” <i>PLoS Biology</i>, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. 2022;20(12):e3001889. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>","chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>.","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","apa":"Mlynarski, W. F., &#38; Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>"},"date_updated":"2023-08-03T14:23:49Z","type":"journal_article","file_date_updated":"2023-01-23T08:46:40Z","oa_version":"Published Version","ec_funded":1,"doi":"10.1371/journal.pbio.3001889","article_type":"original","intvolume":"        20","title":"Efficient coding theory of dynamic attentional modulation","acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","language":[{"iso":"eng"}],"year":"2022","article_processing_charge":"No","publication":"PLoS Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","_id":"12332","abstract":[{"text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments.","lang":"eng"}],"volume":20,"publication_identifier":{"eissn":["1545-7885"]},"project":[{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000925192000001"]},"author":[{"last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"oa":1,"issue":"12","quality_controlled":"1","department":[{"_id":"GaTk"}],"isi":1,"day":"21","status":"public","date_created":"2023-01-22T23:00:55Z","page":"e3001889","file":[{"success":1,"date_created":"2023-01-23T08:46:40Z","checksum":"5d7f1111a87e5f2c1bf92f8886738894","access_level":"open_access","file_name":"2022_PloSBiology_Mlynarski.pdf","file_id":"12337","relation":"main_file","content_type":"application/pdf","file_size":4248838,"date_updated":"2023-01-23T08:46:40Z","creator":"dernst"}],"publisher":"Public Library of Science"},{"article_processing_charge":"No","publication":"eLife","language":[{"iso":"eng"}],"year":"2022","acknowledgement":"We are grateful to N Barton, F Kondrashov, M Lagator, M Pleska, R Roemhild, D Siekhaus, and G\r\nTkacik for input on the manuscript and to K Tomasek for help with flow cytometry.","intvolume":"        11","title":"Adaptation dynamics between copynumber and point mutations","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.6974122","relation":"software"}],"record":[{"id":"12339","relation":"research_data","status":"public"}]},"doi":"10.7554/ELIFE.82240","article_type":"original","oa_version":"Published Version","file_date_updated":"2023-01-23T08:56:21Z","citation":{"ieee":"I. Tomanek and C. C. Guet, “Adaptation dynamics between copynumber and point mutations,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Tomanek, Isabella, and Calin C. Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>, vol. 11, e82240, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>.","ama":"Tomanek I, Guet CC. Adaptation dynamics between copynumber and point mutations. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>","ista":"Tomanek I, Guet CC. 2022. Adaptation dynamics between copynumber and point mutations. eLife. 11, e82240.","chicago":"Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>.","apa":"Tomanek, I., &#38; Guet, C. C. (2022). Adaptation dynamics between copynumber and point mutations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>","short":"I. Tomanek, C.C. Guet, ELife 11 (2022)."},"has_accepted_license":"1","date_updated":"2023-08-03T14:23:07Z","type":"journal_article","article_number":"e82240","date_published":"2022-12-22T00:00:00Z","month":"12","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","publisher":"eLife Sciences Publications","file":[{"success":1,"date_created":"2023-01-23T08:56:21Z","checksum":"9321fd5f06ff59d5e2d33daee84b3da1","access_level":"open_access","file_name":"2022_eLife_Tomanek.pdf","file_id":"12338","relation":"main_file","content_type":"application/pdf","file_size":8835954,"date_updated":"2023-01-23T08:56:21Z","creator":"dernst"}],"status":"public","date_created":"2023-01-22T23:00:55Z","isi":1,"day":"22","department":[{"_id":"CaGu"}],"quality_controlled":"1","oa":1,"external_id":{"isi":["000912674700001"]},"author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","orcid":"0000-0001-6197-363X","first_name":"Isabella","full_name":"Tomanek, Isabella"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"volume":11,"publication_identifier":{"eissn":["2050-084X"]},"abstract":[{"lang":"eng","text":"Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales."}],"_id":"12333","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published"},{"type":"research_data_reference","citation":{"ama":"Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. 2022. doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>","mla":"Tomanek, Isabella, and Calin C. Guet. <i>Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>.","ieee":"I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose.” Dryad, 2022.","short":"I. Tomanek, C.C. Guet, (2022).","apa":"Tomanek, I., &#38; Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>","chicago":"Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>.","ista":"Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose, Dryad, <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>."},"date_updated":"2023-08-03T14:23:06Z","abstract":[{"lang":"eng","text":"Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales."}],"_id":"12339","ddc":["570"],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-23T00:00:00Z","doi":"10.5061/dryad.rfj6q57ds","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X","last_name":"Tomanek","first_name":"Isabella","full_name":"Tomanek, Isabella"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12333"}]},"oa_version":"Published Version","day":"23","department":[{"_id":"CaGu"}],"title":"Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose","main_file_link":[{"url":"https://doi.org/10.5061/dryad.rfj6q57ds","open_access":"1"}],"oa":1,"article_processing_charge":"No","publisher":"Dryad","date_created":"2023-01-23T09:00:37Z","status":"public","year":"2022"},{"ec_funded":1,"doi":"10.15479/at:ista:12103","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11736"},{"status":"public","relation":"part_of_dissertation","id":"9818"},{"id":"8385","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"file_date_updated":"2023-02-02T09:39:25Z","supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"oa_version":"Published Version","type":"dissertation","citation":{"apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>."},"date_updated":"2024-02-28T12:57:46Z","has_accepted_license":"1","ddc":["000","620"],"date_published":"2022-09-22T00:00:00Z","month":"09","article_processing_charge":"No","acknowledged_ssus":[{"_id":"SSU"}],"year":"2022","language":[{"iso":"eng"}],"degree_awarded":"PhD","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg"}],"publication_identifier":{"isbn":["978-3-99078-020-6"],"issn":["2663-337X"]},"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"_id":"12358","abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"138","file":[{"title":"Thesis","relation":"main_file","file_id":"12371","creator":"cchlebak","date_updated":"2023-02-02T09:29:57Z","file_size":104497530,"content_type":"application/pdf","checksum":"083722acbb8115e52e3b0fdec6226769","date_created":"2023-01-25T12:04:41Z","description":"This is the main PDF file of the thesis. File size: 105 MB","file_name":"thesis_gsperl.pdf","access_level":"open_access"},{"relation":"main_file","file_id":"12483","title":"Thesis (compressed 23MB)","file_size":23183710,"content_type":"application/pdf","creator":"cchlebak","date_updated":"2023-02-02T09:33:37Z","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","checksum":"511f82025e5fcb70bff4731d6896ca07","date_created":"2023-02-02T09:33:37Z","file_name":"thesis_gsperl_compressed.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"12484","file_size":98382247,"content_type":"application/x-zip-compressed","creator":"cchlebak","date_updated":"2023-02-02T09:39:25Z","checksum":"ed4cb85225eedff761c25bddfc37a2ed","date_created":"2023-02-02T09:39:25Z","file_name":"thesis-source.zip","access_level":"open_access"}],"publisher":"Institute of Science and Technology Austria","date_created":"2023-01-24T10:49:46Z","status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"day":"22","oa":1},{"day":"19","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"152","file":[{"file_id":"12365","relation":"main_file","content_type":"application/pdf","file_size":20457465,"creator":"cchlebak","date_updated":"2023-09-20T22:30:03Z","date_created":"2023-01-24T13:15:45Z","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","embargo":"2023-09-19","access_level":"open_access","file_name":"220923_Thesis_CDotter_Final.pdf"},{"file_name":"latex_source_CDotter_Thesis_2022.zip","access_level":"closed","checksum":"ad01bb20da163be6893b7af832e58419","date_created":"2023-02-02T09:15:35Z","file_size":22433512,"content_type":"application/x-zip-compressed","date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","relation":"source_file","embargo_to":"open_access","file_id":"12482"}],"date_created":"2023-01-24T13:09:57Z","status":"public","abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"_id":"12364","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"}],"project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964"},{"call_identifier":"H2020","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"FWF","grant_number":"I04205","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"publication_identifier":{"issn":["2663-337X"]},"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","article_processing_charge":"No","degree_awarded":"PhD","year":"2022","language":[{"iso":"eng"}],"type":"dissertation","citation":{"ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>"},"has_accepted_license":"1","date_updated":"2023-11-16T13:10:22Z","ddc":["570"],"month":"09","date_published":"2022-09-19T00:00:00Z","doi":"10.15479/at:ista:12094","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"3"},{"relation":"part_of_dissertation","id":"11160","status":"public"}]},"alternative_title":["ISTA Thesis"],"ec_funded":1,"oa_version":"Published Version","supervisor":[{"first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"file_date_updated":"2023-09-20T22:30:03Z"}]