[{"arxiv":1,"month":"10","article_number":"138","file":[{"file_id":"8976","date_updated":"2020-12-28T08:24:08Z","creator":"dernst","date_created":"2020-12-28T08:24:08Z","file_size":696653,"checksum":"d75359b9814e78d57c0a481b7cde3751","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2020_ElectronJProbab_Redig.pdf","success":1}],"department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” <i>Electronic Journal of Probability</i>, vol. 25.  Institute of Mathematical Statistics, 2020.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>, vol. 25, 138,  Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>.","apa":"Redig, F., Saada, E., &#38; Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>"},"oa_version":"Published Version","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","scopus_import":"1","day":"21","author":[{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico","last_name":"Sau","first_name":"Federico"}],"date_created":"2020-12-27T23:01:17Z","article_type":"original","volume":25,"intvolume":"        25","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"has_accepted_license":"1","file_date_updated":"2020-12-28T08:24:08Z","publication_identifier":{"eissn":["1083-6489"]},"publication_status":"published","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"isi":1,"year":"2020","status":"public","publication":"Electronic Journal of Probability","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","date_published":"2020-10-21T00:00:00Z","ec_funded":1,"publisher":" Institute of Mathematical Statistics","article_processing_charge":"No","doi":"10.1214/20-EJP536","type":"journal_article","_id":"8973","date_updated":"2023-10-17T12:51:56Z","ddc":["510"],"quality_controlled":"1"},{"department":[{"_id":"SiHi"}],"article_number":"100215","file":[{"checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_STARProtocols_Laukoter.pdf","file_id":"8996","creator":"dernst","date_updated":"2021-01-07T15:57:27Z","file_size":4031449,"date_created":"2021-01-07T15:57:27Z"}],"month":"12","citation":{"apa":"Laukoter, S., Amberg, N., Pauler, F., &#38; Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>","mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>, vol. 1, no. 3, 100215, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>.","chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>.","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215.","ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” <i>STAR Protocols</i>, vol. 1, no. 3. Elsevier, 2020.","short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>"},"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":1,"date_created":"2020-12-30T10:17:07Z","article_type":"original","day":"18","author":[{"first_name":"Susanne","last_name":"Laukoter","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","oa_version":"Published Version","file_date_updated":"2021-01-07T15:57:27Z","publication_identifier":{"issn":["2666-1667"]},"publication_status":"published","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":"         1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).","lang":"eng"}],"year":"2020","external_id":{"pmid":["33377108"]},"ec_funded":1,"pmid":1,"date_published":"2020-12-18T00:00:00Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","status":"public","publication":"STAR Protocols","project":[{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F07805"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"_id":"8978","date_updated":"2021-01-12T08:21:36Z","type":"journal_article","article_processing_charge":"No","doi":"10.1016/j.xpro.2020.100215","publisher":"Elsevier","quality_controlled":"1","ddc":["570"]},{"type":"dissertation","date_updated":"2023-09-07T13:24:17Z","_id":"8983","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:8983","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"ddc":["570"],"page":"141","related_material":{"record":[{"id":"8557","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6187"}]},"year":"2020","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","date_published":"2020-12-30T00:00:00Z","status":"public","degree_awarded":"PhD","date_created":"2020-12-30T15:41:26Z","title":"Metabolic regulation of Drosophila macrophage tissue invasion","oa_version":"Published Version","author":[{"last_name":"Emtenani","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","orcid":"0000-0001-6981-6938"}],"day":"30","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2021-12-31T23:30:04Z","abstract":[{"lang":"eng","text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"has_accepted_license":"1","file":[{"checksum":"ec2797ab7a6f253b35df0572b36d1b43","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","file_id":"8984","creator":"semtenan","date_updated":"2021-12-31T23:30:04Z","embargo":"2021-12-30","date_created":"2020-12-30T15:34:01Z","file_size":10848175},{"creator":"semtenan","date_updated":"2021-12-31T23:30:04Z","file_size":10073648,"date_created":"2020-12-30T15:37:36Z","embargo_to":"open_access","file_id":"8985","content_type":"application/pdf","access_level":"closed","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","checksum":"cc30e6608a9815414024cf548dff3b3a","relation":"source_file"}],"department":[{"_id":"DaSi"}],"month":"12","supervisor":[{"orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","last_name":"Siekhaus"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>."},"language":[{"iso":"eng"}],"oa":1},{"doi":"10.1126/sciadv.abc8895","article_processing_charge":"No","publisher":"AAAS","date_updated":"2024-10-29T10:22:43Z","_id":"8986","type":"journal_article","ddc":["580"],"quality_controlled":"1","year":"2020","isi":1,"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"publication":"Science Advances","status":"public","pmid":1,"ec_funded":1,"date_published":"2020-12-11T00:00:00Z","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","author":[{"last_name":"Zhang","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia"},{"last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"last_name":"Zhang","full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","day":"11","title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","oa_version":"Published Version","volume":6,"article_type":"original","date_created":"2021-01-03T23:01:23Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"intvolume":"         6","publication_status":"published","publication_identifier":{"eissn":["2375-2548"]},"file_date_updated":"2021-01-07T12:44:33Z","month":"12","department":[{"_id":"JiFr"}],"file":[{"file_id":"8994","creator":"dernst","date_updated":"2021-01-07T12:44:33Z","date_created":"2021-01-07T12:44:33Z","file_size":10578145,"checksum":"5ac2500b191c08ef6dab5327f40ff663","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_ScienceAdvances_Zhang.pdf"}],"article_number":"eabc8895","oa":1,"language":[{"iso":"eng"}],"issue":"50","citation":{"ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. 2020;6(50). doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” <i>Science Advances</i>, vol. 6, no. 50. AAAS, 2020.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>.","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., &#38; Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"abstract":[{"lang":"eng","text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message."}],"intvolume":"     12578","publication_identifier":{"eissn":["16113349"],"issn":["03029743"],"isbn":["9783030652760"]},"publication_status":"published","author":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"day":"08","scopus_import":"1","title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","oa_version":"Preprint","volume":12578,"date_created":"2021-01-03T23:01:23Z","oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In <i>Progress in Cryptology</i> (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” <i>Progress in Cryptology</i>, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>.","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In <i>Progress in Cryptology</i>, 12578:3–15. LNCS. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in <i>Progress in Cryptology</i>, Bangalore, India, 2020, vol. 12578, pp. 3–15.","short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: <i>Progress in Cryptology</i>. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","department":[{"_id":"KrPi"}],"page":"3-15","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/418"}],"quality_controlled":"1","doi":"10.1007/978-3-030-65277-7_1","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2023-08-24T11:08:58Z","_id":"8987","type":"conference","series_title":"LNCS","project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Progress in Cryptology","ec_funded":1,"date_published":"2020-12-08T00:00:00Z","conference":{"location":"Bangalore, India","name":"INDOCRYPT: International Conference on Cryptology in India","start_date":"2020-12-13","end_date":"2020-12-16"},"year":"2020","isi":1,"external_id":{"isi":["000927592800001"]}},{"_id":"9000","date_updated":"2023-08-24T11:10:22Z","type":"journal_article","article_processing_charge":"No","doi":"10.1073/pnas.2006731117","publisher":"National Academy of Sciences","quality_controlled":"1","page":"31614-31622","ddc":["570"],"isi":1,"year":"2020","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/","description":"News on IST Homepage","relation":"press_release"}]},"external_id":{"pmid":["33268497"],"isi":["000600608300015"]},"pmid":1,"date_published":"2020-12-15T00:00:00Z","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","status":"public","publication":"PNAS","project":[{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"volume":117,"date_created":"2021-01-10T23:01:17Z","article_type":"original","scopus_import":"1","day":"15","author":[{"last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","first_name":"Rok"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"oa_version":"Published Version","title":"Nonequilibrium models of optimal enhancer function","file_date_updated":"2021-01-11T08:37:31Z","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"publication_status":"published","has_accepted_license":"1","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"       117","department":[{"_id":"GaTk"}],"file":[{"file_id":"9004","creator":"dernst","date_updated":"2021-01-11T08:37:31Z","date_created":"2021-01-11T08:37:31Z","file_size":1199247,"checksum":"69039cd402a571983aa6cb4815ffa863","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2020_PNAS_Grah.pdf"}],"month":"12","citation":{"apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>PNAS</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>"},"issue":"50","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]},{"status":"public","publication":"Annals of Mathematics","date_published":"2020-05-01T00:00:00Z","external_id":{"arxiv":["1711.10451"],"isi":["000526986300004"]},"isi":1,"year":"2020","publist_id":"7744","page":"893-948","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.10451"}],"publisher":"Princeton University","article_processing_charge":"No","doi":"10.4007/annals.2020.191.3.4","type":"journal_article","_id":"177","date_updated":"2023-08-17T07:12:37Z","language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"T.D. Browning, W. Sawin, Annals of Mathematics 191 (2020) 893–948.","ieee":"T. D. Browning and W. Sawin, “A geometric version of the circle method,” <i>Annals of Mathematics</i>, vol. 191, no. 3. Princeton University, pp. 893–948, 2020.","ama":"Browning TD, Sawin W. A geometric version of the circle method. <i>Annals of Mathematics</i>. 2020;191(3):893-948. doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>","mla":"Browning, Timothy D., and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>, vol. 191, no. 3, Princeton University, 2020, pp. 893–948, doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>.","apa":"Browning, T. D., &#38; Sawin, W. (2020). A geometric version of the circle method. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>","chicago":"Browning, Timothy D, and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>. Princeton University, 2020. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>.","ista":"Browning TD, Sawin W. 2020. A geometric version of the circle method. Annals of Mathematics. 191(3), 893–948."},"issue":"3","arxiv":1,"month":"05","department":[{"_id":"TiBr"}],"abstract":[{"text":"We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.","lang":"eng"}],"intvolume":"       191","publication_status":"published","oa_version":"Preprint","title":"A geometric version of the circle method","day":"01","author":[{"first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sawin","full_name":"Sawin, Will","first_name":"Will"}],"date_created":"2018-12-11T11:45:02Z","article_type":"original","volume":191},{"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"16","citation":{"ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” <i>Duke Mathematical Journal</i>, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. 2020;169(16):3099-3165. doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>","apa":"Browning, T. D., &#38; Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>. Duke University Press, 2020. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>."},"arxiv":1,"month":"09","department":[{"_id":"TiBr"}],"intvolume":"       169","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"publication_status":"published","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","oa_version":"Preprint","author":[{"first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D"},{"first_name":"Roger","full_name":"Heath Brown, Roger","last_name":"Heath Brown"}],"day":"10","article_type":"original","date_created":"2018-12-11T11:45:02Z","volume":169,"publication":"Duke Mathematical Journal","status":"public","date_published":"2020-09-10T00:00:00Z","external_id":{"isi":["000582676300002"],"arxiv":["1805.10715"]},"year":"2020","isi":1,"page":"3099-3165","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"publisher":"Duke University Press","doi":"10.1215/00127094-2020-0031","article_processing_charge":"No","type":"journal_article","date_updated":"2023-10-17T12:51:10Z","_id":"179"},{"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       374","abstract":[{"text":"While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.\r\n","lang":"eng"}],"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"publication_status":"published","file_date_updated":"2020-07-14T12:47:35Z","author":[{"orcid":"0000-0002-1071-6091","first_name":"Niels P","last_name":"Benedikter","full_name":"Benedikter, Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"last_name":"Porta","full_name":"Porta, Marcello","first_name":"Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"day":"01","scopus_import":"1","title":"Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime","oa_version":"Published Version","volume":374,"article_type":"original","date_created":"2019-07-18T13:30:04Z","oa":1,"language":[{"iso":"eng"}],"citation":{"short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications in Mathematical Physics 374 (2020) 2097–2150.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime,” <i>Communications in Mathematical Physics</i>, vol. 374. Springer Nature, pp. 2097–2150, 2020.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. <i>Communications in Mathematical Physics</i>. 2020;374:2097–2150. doi:<a href=\"https://doi.org/10.1007/s00220-019-03505-5\">10.1007/s00220-019-03505-5</a>","mla":"Benedikter, Niels P., et al. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>, vol. 374, Springer Nature, 2020, pp. 2097–2150, doi:<a href=\"https://doi.org/10.1007/s00220-019-03505-5\">10.1007/s00220-019-03505-5</a>.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2020). Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03505-5\">https://doi.org/10.1007/s00220-019-03505-5</a>","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03505-5\">https://doi.org/10.1007/s00220-019-03505-5</a>.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2020. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. 374, 2097–2150."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"03","arxiv":1,"department":[{"_id":"RoSe"}],"file":[{"file_id":"6668","date_updated":"2020-07-14T12:47:35Z","creator":"dernst","file_size":853289,"date_created":"2019-07-24T07:19:10Z","checksum":"f9dd6dd615a698f1d3636c4a092fed23","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2019_CommMathPhysics_Benedikter.pdf"}],"page":"2097–2150","ddc":["530"],"quality_controlled":"1","doi":"10.1007/s00220-019-03505-5","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2023-08-17T13:51:50Z","_id":"6649","type":"journal_article","project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Communications in Mathematical Physics","ec_funded":1,"date_published":"2020-03-01T00:00:00Z","isi":1,"year":"2020","external_id":{"arxiv":["1809.01902"],"isi":["000527910700019"]}},{"date_published":"2020-12-11T00:00:00Z","publication":"Annals of Statistics","status":"public","isi":1,"year":"2020","external_id":{"isi":["000598369200021"],"arxiv":["1901.01375"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01375"}],"quality_controlled":"1","page":"3619-3642","_id":"6748","date_updated":"2024-03-06T08:28:50Z","type":"journal_article","article_processing_charge":"No","doi":"10.1214/20-AOS1945","publisher":"Institute of Mathematical Statistics","citation":{"ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. 2020;48(6):3619-3642. doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>","ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” <i>Annals of Statistics</i>, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>.","apa":"Javanmard, A., Mondelli, M., &#38; Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>","mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>."},"issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MaMo"}],"arxiv":1,"month":"12","publication_identifier":{"issn":["1932-6157"],"eissn":["1941-7330"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge."}],"intvolume":"        48","volume":48,"date_created":"2019-07-31T09:39:42Z","article_type":"original","day":"11","author":[{"first_name":"Adel","full_name":"Javanmard, Adel","last_name":"Javanmard"},{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"first_name":"Andrea","full_name":"Montanari, Andrea","last_name":"Montanari"}],"title":"Analysis of a two-layer neural network via displacement convexity","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020) 42–55.","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” <i>Theoretical Computer Science</i>, vol. 807. Elsevier, pp. 42–55, 2020.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. <i>Theoretical Computer Science</i>. 2020;807:42-55. doi:<a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">10.1016/j.tcs.2019.06.031</a>","mla":"Avni, Guy, et al. “Dynamic Resource Allocation Games.” <i>Theoretical Computer Science</i>, vol. 807, Elsevier, 2020, pp. 42–55, doi:<a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">10.1016/j.tcs.2019.06.031</a>.","apa":"Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2020). Dynamic resource allocation games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">https://doi.org/10.1016/j.tcs.2019.06.031</a>","ista":"Avni G, Henzinger TA, Kupferman O. 2020. Dynamic resource allocation games. Theoretical Computer Science. 807, 42–55.","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games.” <i>Theoretical Computer Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.tcs.2019.06.031\">https://doi.org/10.1016/j.tcs.2019.06.031</a>."},"month":"02","file":[{"file_size":1413001,"date_created":"2020-10-09T06:31:22Z","date_updated":"2020-10-09T06:31:22Z","creator":"dernst","file_id":"8639","file_name":"2020_TheoreticalCS_Avni.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e86635417f45eb2cd75778f91382f737"}],"department":[{"_id":"ToHe"}],"intvolume":"       807","abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["03043975"]},"file_date_updated":"2020-10-09T06:31:22Z","oa_version":"Submitted Version","title":"Dynamic resource allocation games","author":[{"first_name":"Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"day":"06","scopus_import":"1","article_type":"original","date_created":"2019-08-04T21:59:20Z","volume":807,"project":[{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"publication":"Theoretical Computer Science","status":"public","date_published":"2020-02-06T00:00:00Z","external_id":{"isi":["000512219400004"]},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1341"}]},"year":"2020","isi":1,"ddc":["000"],"page":"42-55","quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.tcs.2019.06.031","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-17T13:52:49Z","_id":"6761"},{"status":"public","publication":"Hippocampus","pmid":1,"date_published":"2020-04-01T00:00:00Z","year":"2020","isi":1,"external_id":{"pmid":["31339190"],"isi":["000477299600001"]},"page":"302-313","ddc":["570"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1002/hipo.23144","publisher":"Wiley","_id":"6796","date_updated":"2023-08-17T13:53:14Z","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Stella F, Urdapilleta E, Luo Y, Treves A. Partial coherence and frustration in self-organizing spherical grids. <i>Hippocampus</i>. 2020;30(4):302-313. doi:<a href=\"https://doi.org/10.1002/hipo.23144\">10.1002/hipo.23144</a>","short":"F. Stella, E. Urdapilleta, Y. Luo, A. Treves, Hippocampus 30 (2020) 302–313.","ieee":"F. Stella, E. Urdapilleta, Y. Luo, and A. Treves, “Partial coherence and frustration in self-organizing spherical grids,” <i>Hippocampus</i>, vol. 30, no. 4. Wiley, pp. 302–313, 2020.","chicago":"Stella, Federico, Eugenio Urdapilleta, Yifan Luo, and Alessandro Treves. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” <i>Hippocampus</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/hipo.23144\">https://doi.org/10.1002/hipo.23144</a>.","ista":"Stella F, Urdapilleta E, Luo Y, Treves A. 2020. Partial coherence and frustration in self-organizing spherical grids. Hippocampus. 30(4), 302–313.","mla":"Stella, Federico, et al. “Partial Coherence and Frustration in Self-Organizing Spherical Grids.” <i>Hippocampus</i>, vol. 30, no. 4, Wiley, 2020, pp. 302–13, doi:<a href=\"https://doi.org/10.1002/hipo.23144\">10.1002/hipo.23144</a>.","apa":"Stella, F., Urdapilleta, E., Luo, Y., &#38; Treves, A. (2020). Partial coherence and frustration in self-organizing spherical grids. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23144\">https://doi.org/10.1002/hipo.23144</a>"},"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","department":[{"_id":"JoCs"}],"file":[{"file_id":"6800","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:53:33Z","file_size":2370658,"checksum":"7b54d22bfbfc0d1188a9ea24d985bfb2","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2019_Hippocampus_Stella.pdf"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        30","file_date_updated":"2020-07-14T12:47:40Z","publication_identifier":{"eissn":["10981063"],"issn":["10509631"]},"publication_status":"published","day":"01","scopus_import":"1","author":[{"first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","last_name":"Stella"},{"first_name":"Eugenio","last_name":"Urdapilleta","full_name":"Urdapilleta, Eugenio"},{"full_name":"Luo, Yifan","last_name":"Luo","first_name":"Yifan"},{"first_name":"Alessandro","full_name":"Treves, Alessandro","last_name":"Treves"}],"title":"Partial coherence and frustration in self-organizing spherical grids","oa_version":"Published Version","volume":30,"date_created":"2019-08-11T21:59:24Z","article_type":"original"},{"oa_version":"Submitted Version","title":"Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens","author":[{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2019-08-12T16:36:32Z","volume":174,"intvolume":"       174","abstract":[{"lang":"eng","text":"Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions."}],"publication_identifier":{"issn":["1046-2023"]},"publication_status":"published","month":"03","department":[{"_id":"JoDa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","citation":{"ieee":"W. Jahr, P. Velicky, and J. G. Danzl, “Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens,” <i>Methods</i>, vol. 174, no. 3. Elsevier, pp. 27–41, 2020.","short":"W. Jahr, P. Velicky, J.G. Danzl, Methods 174 (2020) 27–41.","ama":"Jahr W, Velicky P, Danzl JG. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>. 2020;174(3):27-41. doi:<a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">10.1016/j.ymeth.2019.07.019</a>","apa":"Jahr, W., Velicky, P., &#38; Danzl, J. G. (2020). Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. <i>Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">https://doi.org/10.1016/j.ymeth.2019.07.019</a>","mla":"Jahr, Wiebke, et al. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” <i>Methods</i>, vol. 174, no. 3, Elsevier, 2020, pp. 27–41, doi:<a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">10.1016/j.ymeth.2019.07.019</a>.","ista":"Jahr W, Velicky P, Danzl JG. 2020. Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods. 174(3), 27–41.","chicago":"Jahr, Wiebke, Philipp Velicky, and Johann G Danzl. “Strategies to Maximize Performance in STimulated Emission Depletion (STED) Nanoscopy of Biological Specimens.” <i>Methods</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.ymeth.2019.07.019\">https://doi.org/10.1016/j.ymeth.2019.07.019</a>."},"publisher":"Elsevier","doi":"10.1016/j.ymeth.2019.07.019","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-17T13:59:57Z","_id":"6808","page":"27-41","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100895/","open_access":"1"}],"external_id":{"isi":["000525860400005"],"pmid":["31344404"]},"isi":1,"year":"2020","project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"publication":"Methods","status":"public","date_published":"2020-03-01T00:00:00Z","pmid":1},{"year":"2020","isi":1,"external_id":{"arxiv":["1812.03086"],"isi":["000536053300012"]},"ec_funded":1,"date_published":"2020-06-01T00:00:00Z","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"publication":"Communications in Mathematical Physics","status":"public","date_updated":"2024-02-22T13:33:02Z","_id":"6906","type":"journal_article","doi":"10.1007/s00220-019-03555-9","article_processing_charge":"No","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.03086"}],"quality_controlled":"1","page":"1311-1395","department":[{"_id":"RoSe"}],"month":"06","arxiv":1,"citation":{"mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” <i>Communications in Mathematical Physics</i>, vol. 376, Springer, 2020, pp. 1311–95, doi:<a href=\"https://doi.org/10.1007/s00220-019-03555-9\">10.1007/s00220-019-03555-9</a>.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., &#38; Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-019-03555-9\">https://doi.org/10.1007/s00220-019-03555-9</a>","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” <i>Communications in Mathematical Physics</i>. Springer, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03555-9\">https://doi.org/10.1007/s00220-019-03555-9</a>.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” <i>Communications in Mathematical Physics</i>, vol. 376. Springer, pp. 1311–1395, 2020.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. <i>Communications in Mathematical Physics</i>. 2020;376:1311-1395. doi:<a href=\"https://doi.org/10.1007/s00220-019-03555-9\">10.1007/s00220-019-03555-9</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":376,"article_type":"original","date_created":"2019-09-24T17:30:59Z","author":[{"full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara"},{"full_name":"Brennecke, Christian","last_name":"Brennecke","first_name":"Christian"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"scopus_import":"1","day":"01","oa_version":"Preprint","title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"intvolume":"       376","abstract":[{"text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential.","lang":"eng"}]},{"status":"public","publication":"Reliability Engineering and System Safety","project":[{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-01-01T00:00:00Z","acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"external_id":{"arxiv":["1712.09692"],"isi":["000501641400050"]},"isi":1,"year":"2020","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.09692"}],"publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.ress.2019.106665","type":"journal_article","_id":"6918","date_updated":"2024-03-25T23:30:18Z","language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. <i>Reliability Engineering and System Safety</i>. 2020;193. doi:<a href=\"https://doi.org/10.1016/j.ress.2019.106665\">10.1016/j.ress.2019.106665</a>","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” <i>Reliability Engineering and System Safety</i>, vol. 193. Elsevier, 2020.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering and System Safety</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.ress.2019.106665\">https://doi.org/10.1016/j.ress.2019.106665</a>.","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","apa":"Goharshady, A. K., &#38; Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. <i>Reliability Engineering and System Safety</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ress.2019.106665\">https://doi.org/10.1016/j.ress.2019.106665</a>","mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering and System Safety</i>, vol. 193, 106665, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.ress.2019.106665\">10.1016/j.ress.2019.106665</a>."},"arxiv":1,"month":"01","article_number":"106665","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem."}],"intvolume":"       193","publication_identifier":{"issn":["09518320"]},"publication_status":"published","title":"An efficient algorithm for computing network reliability in small treewidth","oa_version":"Preprint","scopus_import":"1","day":"01","author":[{"last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"}],"date_created":"2019-09-29T22:00:44Z","article_type":"original","volume":193},{"date_updated":"2024-02-22T14:57:30Z","_id":"6944","type":"journal_article","doi":"10.1007/s11263-019-01232-x","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","quality_controlled":"1","page":"970-995","ddc":["004"],"isi":1,"year":"2020","external_id":{"isi":["000494406800001"]},"related_material":{"link":[{"url":"https://doi.org/10.1007/s11263-019-01262-5","relation":"erratum"}],"record":[{"status":"public","relation":"earlier_version","id":"6482"}]},"ec_funded":1,"date_published":"2020-04-01T00:00:00Z","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"status":"public","publication":"International Journal of Computer Vision","volume":128,"article_type":"original","date_created":"2019-10-14T09:14:28Z","author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"scopus_import":"1","day":"01","title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","oa_version":"Published Version","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"publication_status":"published","file_date_updated":"2020-07-14T12:47:45Z","has_accepted_license":"1","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       128","department":[{"_id":"ChLa"}],"file":[{"date_updated":"2020-07-14T12:47:45Z","creator":"dernst","date_created":"2019-11-26T10:30:02Z","file_size":1715072,"file_id":"7110","content_type":"application/pdf","access_level":"open_access","file_name":"2019_IJCV_Sun.pdf","checksum":"155e63edf664dcacb3bdc1c2223e606f","relation":"main_file"}],"month":"04","issue":"4","citation":{"chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” <i>International Journal of Computer Vision</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11263-019-01232-x\">https://doi.org/10.1007/s11263-019-01232-x</a>.","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.","apa":"Sun, R., &#38; Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-019-01232-x\">https://doi.org/10.1007/s11263-019-01232-x</a>","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” <i>International Journal of Computer Vision</i>, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:<a href=\"https://doi.org/10.1007/s11263-019-01232-x\">10.1007/s11263-019-01232-x</a>.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. <i>International Journal of Computer Vision</i>. 2020;128(4):970-995. doi:<a href=\"https://doi.org/10.1007/s11263-019-01232-x\">10.1007/s11263-019-01232-x</a>","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” <i>International Journal of Computer Vision</i>, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"doi":"10.1007/s11263-019-01219-8","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","date_updated":"2023-08-17T14:01:16Z","_id":"6952","type":"journal_article","page":"835-854","ddc":["004"],"quality_controlled":"1","isi":1,"year":"2020","external_id":{"isi":["000491042100002"],"arxiv":["1901.06447"]},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"International Journal of Computer Vision","status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","date_published":"2020-04-01T00:00:00Z","author":[{"first_name":"Paul M","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson"},{"first_name":"Vittorio","last_name":"Ferrari","full_name":"Ferrari, Vittorio"}],"scopus_import":"1","day":"01","oa_version":"Published Version","title":"Learning single-image 3D reconstruction by generative modelling of shape, pose and shading","volume":128,"article_type":"original","date_created":"2019-10-17T13:38:20Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn."}],"intvolume":"       128","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]},"publication_status":"published","file_date_updated":"2020-07-14T12:47:46Z","month":"04","arxiv":1,"department":[{"_id":"ChLa"}],"file":[{"relation":"main_file","checksum":"a0f05dd4f5f64e4f713d8d9d4b5b1e3f","file_name":"2019_CompVision_Henderson.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"6973","file_size":2243134,"date_created":"2019-10-25T10:28:29Z","creator":"dernst","date_updated":"2020-07-14T12:47:46Z"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Henderson PM, Ferrari V. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. <i>International Journal of Computer Vision</i>. 2020;128:835-854. doi:<a href=\"https://doi.org/10.1007/s11263-019-01219-8\">10.1007/s11263-019-01219-8</a>","ieee":"P. M. Henderson and V. Ferrari, “Learning single-image 3D reconstruction by generative modelling of shape, pose and shading,” <i>International Journal of Computer Vision</i>, vol. 128. Springer Nature, pp. 835–854, 2020.","short":"P.M. Henderson, V. Ferrari, International Journal of Computer Vision 128 (2020) 835–854.","ista":"Henderson PM, Ferrari V. 2020. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 128, 835–854.","chicago":"Henderson, Paul M, and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” <i>International Journal of Computer Vision</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11263-019-01219-8\">https://doi.org/10.1007/s11263-019-01219-8</a>.","apa":"Henderson, P. M., &#38; Ferrari, V. (2020). Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-019-01219-8\">https://doi.org/10.1007/s11263-019-01219-8</a>","mla":"Henderson, Paul M., and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” <i>International Journal of Computer Vision</i>, vol. 128, Springer Nature, 2020, pp. 835–54, doi:<a href=\"https://doi.org/10.1007/s11263-019-01219-8\">10.1007/s11263-019-01219-8</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Auxin guides roots to avoid obstacles during gravitropic growth","oa_version":"Published Version","scopus_import":"1","day":"01","author":[{"last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"date_created":"2019-11-12T11:41:32Z","article_type":"original","volume":225,"intvolume":"       225","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","file_date_updated":"2020-11-18T16:42:48Z","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"month":"02","file":[{"file_id":"8772","file_size":717345,"date_created":"2020-11-18T16:42:48Z","creator":"dernst","date_updated":"2020-11-18T16:42:48Z","relation":"main_file","checksum":"cd42ffdb381fd52812b9583d4d407139","file_name":"2020_NewPhytologist_Zhang.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16203\">https://doi.org/10.1111/nph.16203</a>.","ista":"Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 1049–1052.","apa":"Zhang, Y., &#38; Friml, J. (2020). Auxin guides roots to avoid obstacles during gravitropic growth. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16203\">https://doi.org/10.1111/nph.16203</a>","mla":"Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” <i>New Phytologist</i>, vol. 225, no. 3, Wiley, 2020, pp. 1049–52, doi:<a href=\"https://doi.org/10.1111/nph.16203\">10.1111/nph.16203</a>.","ama":"Zhang Y, Friml J. Auxin guides roots to avoid obstacles during gravitropic growth. <i>New Phytologist</i>. 2020;225(3):1049-1052. doi:<a href=\"https://doi.org/10.1111/nph.16203\">10.1111/nph.16203</a>","ieee":"Y. Zhang and J. Friml, “Auxin guides roots to avoid obstacles during gravitropic growth,” <i>New Phytologist</i>, vol. 225, no. 3. Wiley, pp. 1049–1052, 2020.","short":"Y. Zhang, J. Friml, New Phytologist 225 (2020) 1049–1052."},"issue":"3","publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/nph.16203","type":"journal_article","_id":"6997","date_updated":"2023-08-17T14:01:49Z","ddc":["580"],"page":"1049-1052","quality_controlled":"1","external_id":{"isi":["000489638800001"],"pmid":["31603260"]},"isi":1,"year":"2020","status":"public","publication":"New Phytologist","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"date_published":"2020-02-01T00:00:00Z","ec_funded":1,"pmid":1},{"article_processing_charge":"No","doi":"10.1007/s00220-019-03575-5","publisher":"Springer Nature","_id":"7004","date_updated":"2023-08-17T14:02:59Z","type":"journal_article","page":"1803-1873","main_file_link":[{"url":"https://arxiv.org/abs/1810.10402","open_access":"1"}],"quality_controlled":"1","isi":1,"year":"2020","external_id":{"isi":["000536255500004"],"arxiv":["1810.10402"]},"status":"public","publication":"Communications in Mathematical Physics","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"date_published":"2020-06-01T00:00:00Z","scopus_import":"1","day":"01","author":[{"full_name":"Rapcak, Miroslav","last_name":"Rapcak","first_name":"Miroslav"},{"last_name":"Soibelman","full_name":"Soibelman, Yan","first_name":"Yan"},{"full_name":"Yang, Yaping","last_name":"Yang","first_name":"Yaping"},{"first_name":"Gufang","last_name":"Zhao","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"}],"title":"Cohomological Hall algebras, vertex algebras and instantons","oa_version":"Preprint","volume":376,"date_created":"2019-11-12T14:01:27Z","article_type":"original","abstract":[{"text":"We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.","lang":"eng"}],"intvolume":"       376","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"publication_status":"published","month":"06","arxiv":1,"department":[{"_id":"TaHa"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Rapcak M, Soibelman Y, Yang Y, Zhao G. Cohomological Hall algebras, vertex algebras and instantons. <i>Communications in Mathematical Physics</i>. 2020;376:1803-1873. doi:<a href=\"https://doi.org/10.1007/s00220-019-03575-5\">10.1007/s00220-019-03575-5</a>","ieee":"M. Rapcak, Y. Soibelman, Y. Yang, and G. Zhao, “Cohomological Hall algebras, vertex algebras and instantons,” <i>Communications in Mathematical Physics</i>, vol. 376. Springer Nature, pp. 1803–1873, 2020.","short":"M. Rapcak, Y. Soibelman, Y. Yang, G. Zhao, Communications in Mathematical Physics 376 (2020) 1803–1873.","ista":"Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873.","chicago":"Rapcak, Miroslav, Yan Soibelman, Yaping Yang, and Gufang Zhao. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03575-5\">https://doi.org/10.1007/s00220-019-03575-5</a>.","apa":"Rapcak, M., Soibelman, Y., Yang, Y., &#38; Zhao, G. (2020). Cohomological Hall algebras, vertex algebras and instantons. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03575-5\">https://doi.org/10.1007/s00220-019-03575-5</a>","mla":"Rapcak, Miroslav, et al. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” <i>Communications in Mathematical Physics</i>, vol. 376, Springer Nature, 2020, pp. 1803–73, doi:<a href=\"https://doi.org/10.1007/s00220-019-03575-5\">10.1007/s00220-019-03575-5</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"page":"1070–1084","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1007/s12035-019-01783-7","publisher":"Springer Nature","_id":"7033","date_updated":"2023-08-17T14:05:48Z","type":"journal_article","status":"public","publication":"Molecular Neurobiology","pmid":1,"acknowledgement":"This work was supported by National Eye Institute grants R01 EY012223 (RWN), R01 EY030123 (RWN), T32 EY027721 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), and a Vision Science Core grant P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), an unrestricted funding grant from Research to Prevent Blindness (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), the Frederick A. Davis Endowment (RWN), and the Mr. and Mrs. George Taylor Foundation (RWN).","date_published":"2020-02-01T00:00:00Z","isi":1,"year":"2020","external_id":{"pmid":["31673950"],"isi":["000493754200001"]},"intvolume":"        57","abstract":[{"text":"Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality.","lang":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1559-1182"],"issn":["0893-7648"]},"day":"01","scopus_import":"1","author":[{"full_name":"Donahue, RJ","last_name":"Donahue","first_name":"RJ"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","last_name":"Maes","orcid":"0000-0001-9642-1085","first_name":"Margaret E"},{"full_name":"Grosser, JA","last_name":"Grosser","first_name":"JA"},{"first_name":"RW","last_name":"Nickells","full_name":"Nickells, RW"}],"title":"BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage","oa_version":"Submitted Version","volume":57,"date_created":"2019-11-18T14:18:39Z","article_type":"original","oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Donahue, RJ, Margaret E Maes, JA Grosser, and RW Nickells. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” <i>Molecular Neurobiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s12035-019-01783-7\">https://doi.org/10.1007/s12035-019-01783-7</a>.","ista":"Donahue R, Maes ME, Grosser J, Nickells R. 2020. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 57(2), 1070–1084.","mla":"Donahue, RJ, et al. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” <i>Molecular Neurobiology</i>, vol. 57, no. 2, Springer Nature, 2020, pp. 1070–1084, doi:<a href=\"https://doi.org/10.1007/s12035-019-01783-7\">10.1007/s12035-019-01783-7</a>.","apa":"Donahue, R., Maes, M. E., Grosser, J., &#38; Nickells, R. (2020). BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. <i>Molecular Neurobiology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12035-019-01783-7\">https://doi.org/10.1007/s12035-019-01783-7</a>","ama":"Donahue R, Maes ME, Grosser J, Nickells R. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. <i>Molecular Neurobiology</i>. 2020;57(2):1070–1084. doi:<a href=\"https://doi.org/10.1007/s12035-019-01783-7\">10.1007/s12035-019-01783-7</a>","short":"R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084.","ieee":"R. Donahue, M. E. Maes, J. Grosser, and R. Nickells, “BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage,” <i>Molecular Neurobiology</i>, vol. 57, no. 2. Springer Nature, pp. 1070–1084, 2020."},"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"02","department":[{"_id":"SaSi"}]}]