[{"volume":23,"ec_funded":1,"file":[{"creator":"cchlebak","date_updated":"2022-01-24T07:43:09Z","file_size":4794147,"date_created":"2022-01-24T07:43:09Z","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10657","checksum":"77dc540e8011c5475031bdf6ccef20a6","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2329-0501"]},"publication_status":"published","month":"12","intvolume":" 23","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"department":[{"_id":"SaSi"},{"_id":"SiHi"}],"file_date_updated":"2022-01-24T07:43:09Z","ddc":["570"],"date_updated":"2023-11-16T13:12:03Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10655","date_published":"2021-12-10T00:00:00Z","doi":"10.1016/j.omtm.2021.09.006","date_created":"2022-01-23T23:01:28Z","page":"210-224","day":"10","publication":"Molecular Therapy - Methods and Clinical Development","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"first_name":"Gabriele M.","full_name":"Wögenstein, Gabriele M.","last_name":"Wögenstein"},{"last_name":"Colombo","full_name":"Colombo, Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"},{"last_name":"Casado Polanco","full_name":"Casado Polanco, Raquel","orcid":"0000-0001-8293-4568","first_name":"Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd"},{"full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000748748500019"]},"article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006","apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006."},"project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"}]},{"citation":{"ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","article_number":"101012","project":[{"name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2021","day":"17","publication":"STAR Protocols","doi":"10.1016/j.xpro.2021.101012","date_published":"2021-12-17T00:00:00Z","date_created":"2021-12-19T23:01:32Z","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","publisher":"Elsevier ; Cell Press","quality_controlled":"1","oa":1,"date_updated":"2023-11-16T13:11:04Z","ddc":["573"],"department":[{"_id":"SaSi"}],"file_date_updated":"2021-12-20T08:58:40Z","_id":"10565","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["2666-1667"]},"publication_status":"published","file":[{"file_name":"2021_STARProt_Venturino.pdf","date_created":"2021-12-20T08:58:40Z","file_size":6207060,"date_updated":"2021-12-20T08:58:40Z","creator":"cchlebak","success":1,"checksum":"9ea2501056c5df99e84726b845e9b976","file_id":"10570","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"issue":"4","volume":2,"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 2"},{"year":"2021","has_accepted_license":"1","publication":"STAR Protocols","day":"10","date_created":"2021-11-21T23:01:28Z","doi":"10.1016/j.xpro.2021.100939","date_published":"2021-11-10T00:00:00Z","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). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 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.","oa":1,"publisher":"Cell Press","quality_controlled":"1","citation":{"chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939.","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","apa":"Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","article_number":"100939","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","file_id":"10329","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_STARProtocols_Amberg.pdf","date_created":"2021-11-22T08:23:58Z","file_size":7309464,"date_updated":"2021-11-22T08:23:58Z","creator":"cchlebak"}],"ec_funded":1,"issue":"4","volume":2,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021)."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 2","month":"11","date_updated":"2023-11-16T13:08:03Z","ddc":["573"],"department":[{"_id":"SiHi"}],"file_date_updated":"2021-11-22T08:23:58Z","_id":"10321","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"month":"11","intvolume":" 213","scopus_import":"1","file":[{"success":1,"checksum":"6b209e4d44775d4e02b50f78982c15fa","file_id":"10291","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_JournalStructBiol_Dimchev.pdf","date_created":"2021-11-15T13:11:27Z","creator":"cchlebak","file_size":16818304,"date_updated":"2021-11-15T13:11:27Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","issue":"4","related_material":{"record":[{"status":"public","id":"14502","relation":"software"}]},"volume":213,"_id":"10290","status":"public","keyword":["Structural Biology"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["572"],"date_updated":"2023-11-21T08:36:02Z","file_date_updated":"2021-11-15T13:11:27Z","department":[{"_id":"FlSc"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","publisher":"Elsevier ","quality_controlled":"1","oa":1,"day":"03","publication":"Journal of Structural Biology","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1016/j.jsb.2021.107808","date_published":"2021-11-03T00:00:00Z","date_created":"2021-11-15T12:21:42Z","article_number":"107808","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808."},"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","author":[{"last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Behnam","full_name":"Amiri, Behnam","last_name":"Amiri"},{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000720259500002"]}},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04293"}],"month":"06","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths."}],"oa_version":"Submitted Version","related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"publication_identifier":{"eisbn":["978-3-9031-7639-3"],"isbn":["978-1-6654-4501-6"],"eissn":["1861-2288"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2021-06-21","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","name":"2021 IFIP Networking Conference (IFIP Networking)"},"status":"public","_id":"9969","department":[{"_id":"KrPi"}],"date_updated":"2023-11-30T10:54:50Z","quality_controlled":"1","publisher":"IEEE","oa":1,"date_published":"2021-06-21T00:00:00Z","doi":"10.23919/IFIPNetworking52078.2021.9472205","date_created":"2021-08-29T22:01:16Z","isi":1,"year":"2021","day":"21","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"last_name":"Salem","full_name":"Salem, Iosif","first_name":"Iosif"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"},{"first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","last_name":"Yeo"}],"external_id":{"isi":["000853016800008"],"arxiv":["2104.04293"]},"article_processing_charge":"No","title":"LightPIR: Privacy-preserving route discovery for payment channel networks","citation":{"apa":"Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3453483.3454093","date_created":"2021-07-11T22:01:17Z","page":"1033-1048","day":"01","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","isi":1,"year":"2021","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","title":"Proving non-termination by program reversal","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"last_name":"Novotný","full_name":"Novotný, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"article_processing_charge":"No","external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–48, doi:10.1145/3453483.3454093.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021). Proving non-termination by program reversal. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093","ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1033–1048.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048."},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"related_material":{"record":[{"status":"public","id":"14539","relation":"dissertation_contains"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450383912"]},"publication_status":"published","month":"06","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.01189"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters."}],"department":[{"_id":"KrCh"}],"date_updated":"2023-11-30T10:55:37Z","status":"public","type":"conference","conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","location":"Online","end_date":"2021-06-26"},"_id":"9644"},{"date_updated":"2023-12-13T14:47:25Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2021-08-06T06:44:31Z","_id":"9760","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["2521-327X"]},"publication_status":"published","file":[{"file_name":"2021_Quantum_Sack.pdf","date_created":"2021-08-06T06:44:31Z","file_size":2312482,"date_updated":"2021-08-06T06:44:31Z","creator":"cchlebak","file_id":"9774","checksum":"9706c2bb8e748e9b5b138381995a7f6f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":5,"related_material":{"record":[{"relation":"dissertation_contains","id":"14622","status":"public"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing."}],"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 5","citation":{"short":"S. Sack, M. Serbyn, Quantum 5 (2021).","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491","apa":"Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"article_processing_charge":"Yes","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","article_number":"491","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Quantum","doi":"10.22331/Q-2021-07-01-491","date_published":"2021-07-01T00:00:00Z","date_created":"2021-08-01T22:01:21Z","acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","quality_controlled":"1","oa":1},{"article_processing_charge":"No","external_id":{"isi":["000758218600033"],"arxiv":["2108.02188"]},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady"},{"last_name":"Novotný","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Jiří","last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"title":"On lexicographic proof rules for probabilistic termination","citation":{"short":"K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in 24th International Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., & Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In 24th International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual: Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33","ama":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: 24th International Symposium on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” 24th International Symposium on Formal Methods, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic proof rules for probabilistic termination. 24th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In 24th International Symposium on Formal Methods, 13047:619–39. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"page":"619-639","date_created":"2021-12-05T23:01:45Z","doi":"10.1007/978-3-030-90870-6_33","date_published":"2021-11-10T00:00:00Z","year":"2021","isi":1,"publication":"24th International Symposium on Formal Methods","day":"10","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"KrCh"}],"date_updated":"2024-01-17T08:19:41Z","conference":{"name":"FM: Formal Methods","start_date":"2021-11-20","location":"Virtual","end_date":"2021-11-26"},"type":"conference","status":"public","_id":"10414","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"},{"id":"14778","status":"public","relation":"later_version"}]},"volume":13047,"publication_status":"published","publication_identifier":{"eisbn":["978-3-030-90870-6"],"issn":["0302-9743"],"isbn":["9-783-0309-0869-0"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 13047","month":"11","abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"oa_version":"Preprint"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1001-4861"]},"publication_status":"published","issue":"12","volume":37,"oa_version":"Submitted Version","abstract":[{"text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. ","lang":"eng"}],"month":"10","intvolume":" 37","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3866/PKU.WHXB202108017","open_access":"1"}],"date_updated":"2024-01-17T11:29:33Z","department":[{"_id":"MaIb"}],"_id":"14800","status":"public","article_type":"review","type":"journal_article","day":"13","publication":"Acta Physico-Chimica Sinica","year":"2021","doi":"10.3866/PKU.WHXB202108017","date_published":"2021-10-13T00:00:00Z","date_created":"2024-01-14T23:00:58Z","publisher":"Peking University","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017.","chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017.","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. Peking University. https://doi.org/10.3866/PKU.WHXB202108017","ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","ieee":"C. Chang et al., “Recent progress on two-dimensional materials,” Acta Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.","mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021, doi:10.3866/PKU.WHXB202108017."},"title":"Recent progress on two-dimensional materials","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"full_name":"Chen, Wei","last_name":"Chen","first_name":"Wei"},{"full_name":"Chen, Ye","last_name":"Chen","first_name":"Ye"},{"last_name":"Chen","full_name":"Chen, Yonghua","first_name":"Yonghua"},{"first_name":"Yu","full_name":"Chen, Yu","last_name":"Chen"},{"last_name":"Ding","full_name":"Ding, Feng","first_name":"Feng"},{"full_name":"Fan, Chunhai","last_name":"Fan","first_name":"Chunhai"},{"full_name":"Fan, Hong Jin","last_name":"Fan","first_name":"Hong Jin"},{"first_name":"Zhanxi","full_name":"Fan, Zhanxi","last_name":"Fan"},{"first_name":"Cheng","full_name":"Gong, Cheng","last_name":"Gong"},{"full_name":"Gong, Yongji","last_name":"Gong","first_name":"Yongji"},{"full_name":"He, Qiyuan","last_name":"He","first_name":"Qiyuan"},{"first_name":"Xun","full_name":"Hong, Xun","last_name":"Hong"},{"first_name":"Sheng","full_name":"Hu, Sheng","last_name":"Hu"},{"last_name":"Hu","full_name":"Hu, Weida","first_name":"Weida"},{"first_name":"Wei","full_name":"Huang, Wei","last_name":"Huang"},{"first_name":"Yuan","full_name":"Huang, Yuan","last_name":"Huang"},{"full_name":"Ji, Wei","last_name":"Ji","first_name":"Wei"},{"full_name":"Li, Dehui","last_name":"Li","first_name":"Dehui"},{"last_name":"Li","full_name":"Li, Lain Jong","first_name":"Lain Jong"},{"first_name":"Qiang","full_name":"Li, Qiang","last_name":"Li"},{"first_name":"Li","full_name":"Lin, Li","last_name":"Lin"},{"last_name":"Ling","full_name":"Ling, Chongyi","first_name":"Chongyi"},{"full_name":"Liu, Minghua","last_name":"Liu","first_name":"Minghua"},{"first_name":"Nan","full_name":"Liu, Nan","last_name":"Liu"},{"first_name":"Zhuang","full_name":"Liu, Zhuang","last_name":"Liu"},{"first_name":"Kian Ping","last_name":"Loh","full_name":"Loh, Kian Ping"},{"first_name":"Jianmin","full_name":"Ma, Jianmin","last_name":"Ma"},{"full_name":"Miao, Feng","last_name":"Miao","first_name":"Feng"},{"first_name":"Hailin","last_name":"Peng","full_name":"Peng, Hailin"},{"first_name":"Mingfei","full_name":"Shao, Mingfei","last_name":"Shao"},{"full_name":"Song, Li","last_name":"Song","first_name":"Li"},{"first_name":"Shao","full_name":"Su, Shao","last_name":"Su"},{"first_name":"Shuo","last_name":"Sun","full_name":"Sun, Shuo"},{"first_name":"Chaoliang","full_name":"Tan, Chaoliang","last_name":"Tan"},{"full_name":"Tang, Zhiyong","last_name":"Tang","first_name":"Zhiyong"},{"full_name":"Wang, Dingsheng","last_name":"Wang","first_name":"Dingsheng"},{"last_name":"Wang","full_name":"Wang, Huan","first_name":"Huan"},{"last_name":"Wang","full_name":"Wang, 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Han"},{"full_name":"Zhang, Hui","last_name":"Zhang","first_name":"Hui"},{"last_name":"Zhang","full_name":"Zhang, Qichun","first_name":"Qichun"},{"first_name":"Tierui","full_name":"Zhang, Tierui","last_name":"Zhang"},{"last_name":"Zhang","full_name":"Zhang, Xiang","first_name":"Xiang"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"},{"full_name":"Zhao, Meiting","last_name":"Zhao","first_name":"Meiting"},{"full_name":"Zhao, Weijie","last_name":"Zhao","first_name":"Weijie"},{"first_name":"Yunxuan","last_name":"Zhao","full_name":"Zhao, Yunxuan"},{"full_name":"Zhou, Kai Ge","last_name":"Zhou","first_name":"Kai Ge"},{"full_name":"Zhou, Xing","last_name":"Zhou","first_name":"Xing"},{"first_name":"Yu","last_name":"Zhou","full_name":"Zhou, Yu"},{"first_name":"Hongwei","last_name":"Zhu","full_name":"Zhu, Hongwei"},{"first_name":"Hua","last_name":"Zhang","full_name":"Zhang, Hua"},{"first_name":"Zhongfan","full_name":"Liu, Zhongfan","last_name":"Liu"}],"article_processing_charge":"No","article_number":"2108017"},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in 21st International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 42–61.","apa":"Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In 21st International Conference on Runtime Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: 21st International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” 21st International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.","ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In 21st International Conference on Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","first_name":"Anna","last_name":"Lukina","full_name":"Lukina, Anna"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2009.06429"],"isi":["000719383800003"]},"title":"Into the unknown: active monitoring of neural networks","acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"06","publication":"21st International Conference on Runtime Verification","page":"42-61","doi":"10.1007/978-3-030-88494-9_3","date_published":"2021-10-06T00:00:00Z","date_created":"2021-10-31T23:01:31Z","_id":"10206","type":"conference","conference":{"location":"Virtual","end_date":"2021-10-14","start_date":"2021-10-11","name":"RV: Runtime Verification"},"status":"public","keyword":["monitoring","neural networks","novelty detection"],"date_updated":"2024-01-30T12:06:56Z","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios."}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/2009.06429","open_access":"1"}],"month":"10","place":"Cham","publication_identifier":{"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"],"isbn":["9-783-0308-8493-2"],"eissn":["1611-3349"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":"12974 ","related_material":{"record":[{"relation":"extended_version","status":"public","id":"13234"}]},"ec_funded":1},{"date_updated":"2024-02-05T10:02:45Z","department":[{"_id":"RoSe"}],"_id":"14889","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"publication_status":"published","volume":3,"issue":"4","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2."}],"month":"10","intvolume":" 3","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.02098","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676.","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653.","ieee":"N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021.","short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676.","ama":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653","apa":"Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653","mla":"Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653."},"title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron","author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","last_name":"Rademacher"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2005.02098"]},"article_processing_charge":"No","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"day":"01","publication":"Pure and Applied Analysis","year":"2021","doi":"10.2140/paa.2021.3.653","date_published":"2021-10-01T00:00:00Z","date_created":"2024-01-28T23:01:43Z","page":"653-676","acknowledgement":"Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions.","quality_controlled":"1","publisher":"Mathematical Sciences Publishers","oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677.","apa":"Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2021.3.677","ama":"Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677","short":"L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726.","ieee":"L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 677–726, 2021.","chicago":"Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.677.","ista":"Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 677–726."},"title":"Beyond Bogoliubov dynamics","author":[{"orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea","last_name":"Bossmann","first_name":"Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425"},{"last_name":"Petrat","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"},{"full_name":"Soffer, Avy","last_name":"Soffer","first_name":"Avy"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.11004"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","publication":"Pure and Applied Analysis","year":"2021","date_published":"2021-10-01T00:00:00Z","doi":"10.2140/paa.2021.3.677","date_created":"2024-01-28T23:01:43Z","page":"677-726","acknowledgement":"We are grateful for the hospitality of Central China Normal University (CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher, Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research\r\nTraining Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska-Curie Grant Agreement No. 754411.","quality_controlled":"1","publisher":"Mathematical Sciences Publishers","oa":1,"date_updated":"2024-02-05T09:26:31Z","department":[{"_id":"RoSe"}],"_id":"14890","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"publication_status":"published","volume":3,"issue":"4","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.","lang":"eng"}],"month":"10","intvolume":" 3","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1912.11004","open_access":"1"}]},{"department":[{"_id":"LaEr"}],"date_updated":"2024-02-19T08:30:00Z","status":"public","article_type":"original","type":"journal_article","_id":"15013","ec_funded":1,"issue":"2","volume":2,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2690-1005"],"issn":["2690-0998"]},"intvolume":" 2","month":"05","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1907.13631","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge."}],"title":"Spectral radius of random matrices with independent entries","article_processing_charge":"No","external_id":{"arxiv":["1907.13631"]},"author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221","ama":"Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221","short":"J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with independent entries,” Probability and Mathematical Physics, vol. 2, no. 2. Mathematical Sciences Publishers, pp. 221–280, 2021.","mla":"Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221.","ista":"Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random Matrices with Independent Entries.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2024-02-18T23:01:03Z","date_published":"2021-05-21T00:00:00Z","doi":"10.2140/pmp.2021.2.221","page":"221-280","publication":"Probability and Mathematical Physics","day":"21","year":"2021","oa":1,"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","acknowledgement":"Partially supported by ERC Starting Grant RandMat No. 715539 and the SwissMap grant of Swiss National Science Foundation. Partially supported by ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center for Mathematics in Bonn."},{"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"article_number":"e2113046118","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"last_name":"Dahhan","full_name":"Dahhan, Dana A","first_name":"Dana A"},{"last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"full_name":"Mahou, Pierre","last_name":"Mahou","first_name":"Pierre"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Jie","last_name":"Wang","first_name":"Jie"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","first_name":"Juan L","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin"},{"last_name":"van Damme","full_name":"van Damme, Daniël","first_name":"Daniël"},{"first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bednarek, Sebastian Y","last_name":"Bednarek","first_name":"Sebastian Y"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"article_processing_charge":"No","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","citation":{"mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:10.1073/pnas.2113046118.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118","ieee":"A. J. Johnson et al., “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” Proceedings of the National Academy of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","doi":"10.1073/pnas.2113046118","date_published":"2021-12-14T00:00:00Z","date_created":"2021-08-11T14:11:43Z","has_accepted_license":"1","isi":1,"year":"2021","day":"14","publication":"Proceedings of the National Academy of Sciences","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9887","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"file_date_updated":"2021-12-15T08:59:40Z","date_updated":"2024-02-19T11:06:09Z","ddc":["580"],"month":"12","intvolume":" 118","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"},{"id":"14988","status":"public","relation":"research_data"}],"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}]},"volume":118,"issue":"51","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10546","checksum":"8d01e72e22c4fb1584e72d8601947069","success":1,"date_updated":"2021-12-15T08:59:40Z","file_size":2757340,"creator":"cchlebak","date_created":"2021-12-15T08:59:40Z","file_name":"2021_PNAS_Johnson.pdf"}],"language":[{"iso":"eng"}]},{"_id":"14988","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"date_updated":"2024-02-19T11:06:09Z","citation":{"ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","short":"A.J. Johnson, (2021).","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100","mla":"Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo, 2021, doi:10.5281/ZENODO.5747100.","ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.","chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5747100."},"department":[{"_id":"JiFr"}],"title":"Raw data from Johnson et al, PNAS, 2021","article_processing_charge":"No","author":[{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"}],"oa_version":"Published Version","abstract":[{"text":"Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS","lang":"eng"}],"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5747100"}],"publisher":"Zenodo","day":"01","year":"2021","has_accepted_license":"1","date_created":"2024-02-14T14:13:48Z","date_published":"2021-12-01T00:00:00Z","doi":"10.5281/ZENODO.5747100","related_material":{"record":[{"relation":"used_in_publication","id":"9887","status":"public"}]}},{"related_material":{"record":[{"relation":"later_version","status":"public","id":"10851"},{"relation":"research_data","id":"9636","status":"public"}]},"date_published":"2021-07-08T00:00:00Z","date_created":"2021-09-21T08:41:02Z","ec_funded":1,"publication_status":"submitted","year":"2021","day":"08","publication":"arXiv","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03695"}],"oa":1,"month":"07","abstract":[{"text":"Superconductor-semiconductor hybrids are platforms for realizing effective p-wave superconductivity. Spin-orbit coupling, combined with the proximity effect, causes the two-dimensional semiconductor to inherit p±ip intraband pairing, and application of magnetic field can then result in transitions to the normal state, partial Bogoliubov Fermi surfaces, or topological phases with Majorana modes. Experimentally probing the hybrid superconductor-semiconductor interface is challenging due to the shunting effect of the conventional superconductor. Consequently, the nature of induced pairing remains an open question. Here, we use the circuit quantum electrodynamics architecture to probe induced superconductivity in a two dimensional Al-InAs hybrid system. We observe a strong suppression of superfluid density and enhanced dissipation driven by magnetic field, which cannot be accounted for by the depairing theory of an s-wave superconductor. These observations are explained by a picture of independent intraband p±ip superconductors giving way to partial Bogoliubov Fermi surfaces, and allow for the first characterization of key properties of the hybrid superconducting system.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Preprint","acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. JS and AG were supported by funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No.754411.","author":[{"full_name":"Phan, Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T"},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543"},{"first_name":"M.","last_name":"Hatefipour","full_name":"Hatefipour, M."},{"first_name":"W. M.","full_name":"Strickland, W. M.","last_name":"Strickland"},{"last_name":"Shabani","full_name":"Shabani, J.","first_name":"J."},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.03695"]},"department":[{"_id":"MaSe"},{"_id":"AnHi"},{"_id":"MiLe"}],"title":"Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid","date_updated":"2024-02-21T12:36:52Z","citation":{"ista":"Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn M, Higginbotham AP. Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv, 2107.03695.","chicago":"Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland, J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, n.d.","ieee":"D. T. Phan et al., “Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid,” arXiv. .","short":"D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J. Shabani, M. Serbyn, A.P. Higginbotham, ArXiv (n.d.).","ama":"Phan DT, Senior JL, Ghazaryan A, et al. Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv.","apa":"Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M., Shabani, J., … Higginbotham, A. P. (n.d.). Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid. arXiv.","mla":"Phan, Duc T., et al. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, 2107.03695."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"_id":"10029","article_number":"2107.03695"},{"has_accepted_license":"1","year":"2021","file":[{"success":1,"checksum":"635df3c08fc13c3dac008cd421aefbe4","file_id":"9292","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip","date_created":"2021-03-27T13:46:17Z","creator":"gkatsaro","file_size":10616071,"date_updated":"2021-03-27T13:46:17Z"},{"date_created":"2021-04-01T07:52:56Z","file_name":"README.txt","date_updated":"2021-04-01T07:52:56Z","file_size":470,"creator":"dernst","checksum":"12b3ca69ae7509a346711baae0b02a75","file_id":"9302","success":1,"content_type":"text/plain","access_level":"open_access","relation":"main_file"}],"day":"29","doi":"10.15479/AT:ISTA:9291","date_published":"2021-03-29T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2021-03-27T13:47:49Z","abstract":[{"text":"This .zip File contains the transport data for figures presented in the main text and supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","citation":{"ieee":"G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.","short":"G. Katsaros, (2021).","ama":"Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:10.15479/AT:ISTA:9291","apa":"Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291","mla":"Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.","ista":"Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.","chicago":"Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291."},"date_updated":"2024-02-21T12:37:14Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"GeKa"}],"file_date_updated":"2021-04-01T07:52:56Z","title":"Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium","_id":"9291","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria."},"date_updated":"2024-02-21T12:36:52Z","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","department":[{"_id":"AnHi"}],"file_date_updated":"2021-07-07T20:37:28Z","article_processing_charge":"No","author":[{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}],"_id":"9636","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","file":[{"creator":"ahigginb","date_updated":"2021-07-07T20:37:28Z","file_size":3345244,"date_created":"2021-07-07T20:37:28Z","file_name":"figures_data.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"9637","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1}],"year":"2021","has_accepted_license":"1","date_created":"2021-07-07T20:43:10Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","related_material":{"record":[{"status":"public","id":"10029","relation":"used_in_publication"}]},"date_published":"2021-01-01T00:00:00Z","oa_version":"Submitted Version","oa":1,"publisher":"Institute of Science and Technology Austria"},{"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"}],"article_number":"82-88","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini"},{"first_name":"Fernando","full_name":"Peñaranda, Fernando","last_name":"Peñaranda"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Brauns","full_name":"Brauns, Matthias"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krogstrup, Peter","last_name":"Krogstrup","first_name":"Peter"},{"last_name":"San-Jose","full_name":"San-Jose, Pablo","first_name":"Pablo"},{"full_name":"Prada, Elsa","last_name":"Prada","first_name":"Elsa"},{"full_name":"Aguado, Ramón","last_name":"Aguado","first_name":"Ramón"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"external_id":{"arxiv":["2008.02348"],"isi":["000677843100034"]},"article_processing_charge":"No","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","citation":{"mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:10.1126/science.abf1513.","ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 2021;373(6550). doi:10.1126/science.abf1513","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abf1513","ieee":"M. Valentini et al., “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no. 6550. American Association for the Advancement of Science, 2021.","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).","chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” Science. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abf1513.","ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","doi":"10.1126/science.abf1513","date_published":"2021-07-02T00:00:00Z","date_created":"2020-12-02T10:51:52Z","isi":1,"year":"2021","day":"02","publication":"Science","type":"journal_article","article_type":"original","status":"public","_id":"8910","department":[{"_id":"GeKa"},{"_id":"Bio"}],"date_updated":"2024-02-21T12:40:09Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02348"}],"month":"07","intvolume":" 373","abstract":[{"lang":"eng","text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Submitted Version","volume":373,"issue":"6550","related_material":{"link":[{"url":"https://ist.ac.at/en/news/unfinding-a-split-electron/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"13286"},{"relation":"research_data","id":"9389","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["00368075"],"eissn":["10959203"]},"publication_status":"published","language":[{"iso":"eng"}]},{"file":[{"date_updated":"2021-04-14T09:48:47Z","file_size":221832287,"creator":"djirovec","date_created":"2021-04-14T09:48:47Z","file_name":"DataRepositorySTqubit.zip","content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","checksum":"c569d2a2ce1694445cdbca19cf8ae023","file_id":"9324","success":1},{"file_id":"9325","checksum":"845bdf87430718ad6aff47eda7b5fc92","success":1,"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file","date_created":"2021-04-14T09:49:30Z","file_name":"ReadMe","date_updated":"2021-04-14T09:49:30Z","file_size":4323,"creator":"djirovec"}],"day":"14","has_accepted_license":"1","year":"2021","doi":"10.15479/AT:ISTA:9323","date_published":"2021-04-14T00:00:00Z","related_material":{"record":[{"status":"public","id":"8909","relation":"used_in_publication"}]},"contributor":[{"last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Daniel"}],"date_created":"2021-04-14T09:50:22Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python."}],"month":"04","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"date_updated":"2024-02-21T12:39:15Z","citation":{"short":"D. Jirovec, (2021).","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323","mla":"Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323."},"file_date_updated":"2021-04-14T09:49:30Z","title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"author":[{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"}],"article_processing_charge":"No","_id":"9323","status":"public","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"}},{"abstract":[{"text":"This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\".","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","file":[{"file_name":"Notebook_Valentini.pdf","date_created":"2021-05-14T11:42:23Z","creator":"mvalenti","file_size":10572981,"date_updated":"2021-05-14T11:42:23Z","checksum":"80a905c4eef24dab6fb247e81a3d67f5","file_id":"9390","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","file_id":"9391","checksum":"1e61a7e63949448a8db0091cdac23570","date_updated":"2021-05-14T11:56:48Z","file_size":99076111,"creator":"mvalenti","date_created":"2021-05-14T11:56:48Z","file_name":"Experimental_data.zip"}],"date_created":"2021-05-14T12:07:53Z","contributor":[{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","contributor_type":"contact_person"}],"related_material":{"record":[{"id":"8910","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:9389","date_published":"2021-01-01T00:00:00Z","_id":"9389","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","citation":{"ista":"Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389.","chicago":"Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.","short":"M. Valentini, (2021).","ieee":"M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021.","apa":"Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389","ama":"Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389","mla":"Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389."},"date_updated":"2024-02-21T12:40:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_processing_charge":"No","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"}],"file_date_updated":"2021-05-14T11:56:48Z","title":"Research data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\"","department":[{"_id":"GradSch"},{"_id":"GeKa"}]},{"department":[{"_id":"GeKa"}],"file_date_updated":"2021-12-17T08:12:37Z","date_updated":"2024-02-21T12:41:26Z","ddc":["620"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["general engineering"],"status":"public","_id":"10559","ec_funded":1,"related_material":{"record":[{"id":"8831","status":"public","relation":"earlier_version"},{"status":"public","id":"8834","relation":"research_data"}]},"volume":3,"issue":"2","publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10561","checksum":"60a1bc9c9b616b1b155044bb8cfc6484","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_PhysRevResearch_Aggarwal.pdf","date_created":"2021-12-17T08:12:37Z","creator":"cchlebak","file_size":1917512,"date_updated":"2021-12-17T08:12:37Z"}],"scopus_import":"1","intvolume":" 3","month":"04","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Hole gases in planar germanium can have high mobilities in combination with strong spin-orbit interaction and electrically tunable g factors, and are therefore emerging as a promising platform for creating hybrid superconductor-semiconductor devices. A key challenge towards hybrid Ge-based quantum technologies is the design of high-quality interfaces and superconducting contacts that are robust against magnetic fields. In this work, by combining the assets of aluminum, which provides good contact to the Ge, and niobium, which has a significant superconducting gap, we demonstrate highly transparent low-disordered JoFETs with relatively large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["2012.00322"]},"author":[{"last_name":"Aggarwal","orcid":"0000-0001-9985-9293","full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","last_name":"Hofmann"},{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"first_name":"Amir","full_name":"Sammak, Amir","last_name":"Sammak"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"first_name":"Sara","full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez"},{"last_name":"Veldhorst","full_name":"Veldhorst, Menno","first_name":"Menno"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","citation":{"chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005.","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 3(2), L022005.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” Physical Review Research, vol. 3, no. 2, L022005, American Physical Society, 2021, doi:10.1103/physrevresearch.3.l022005.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G. Katsaros, Physical Review Research 3 (2021).","ieee":"K. Aggarwal et al., “Enhancement of proximity-induced superconductivity in a planar Ge hole gas,” Physical Review Research, vol. 3, no. 2. American Physical Society, 2021.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.3.l022005","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 2021;3(2). doi:10.1103/physrevresearch.3.l022005"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"article_number":"L022005","date_created":"2021-12-16T18:50:57Z","date_published":"2021-04-15T00:00:00Z","doi":"10.1103/physrevresearch.3.l022005","year":"2021","has_accepted_license":"1","publication":"Physical Review Research","day":"15","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autnoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges support through FRIPRO-project 274853, which is funded by the Research Council of Norway."},{"abstract":[{"lang":"eng","text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 288","month":"09","publication_status":"published","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"language":[{"iso":"eng"}],"file":[{"checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_id":"10172","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-22T11:48:02Z","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","date_updated":"2021-10-22T11:48:02Z","file_size":995806,"creator":"cchlebak"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"9949","relation":"research_data"}],"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}]},"volume":288,"issue":"1959","_id":"10166","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"status":"public","date_updated":"2024-02-21T12:40:29Z","ddc":["595"],"file_date_updated":"2021-10-22T11:48:02Z","department":[{"_id":"BeVi"}],"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","oa":1,"quality_controlled":"1","publisher":"The Royal Society","year":"2021","isi":1,"has_accepted_license":"1","publication":"Proceedings of the Royal Society B: Biological Sciences","day":"22","date_created":"2021-10-21T07:46:06Z","doi":"10.1098/rspb.2021.1720","date_published":"2021-09-22T00:00:00Z","article_number":"20211720","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720","apa":"Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society, 2021.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2021. https://doi.org/10.1098/rspb.2021.1720."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp"},{"_id":"9192","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9192."},"date_updated":"2024-02-21T12:41:09Z","file_date_updated":"2021-02-24T17:45:13Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","article_processing_charge":"No","author":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"last_name":"Arathoon","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"oa_version":"Published Version","abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"month":"02","oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"f85537815809a8a4b7da9d01163f88c0","file_id":"9193","success":1,"creator":"larathoo","date_updated":"2021-02-24T17:45:13Z","file_size":5934452,"date_created":"2021-02-24T17:45:13Z","file_name":"Data_Code.zip"}],"day":"26","year":"2021","has_accepted_license":"1","date_created":"2021-02-24T17:49:21Z","contributor":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh"},{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Arathoon"},{"last_name":"Baskett","first_name":"Carina","contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","contributor_type":"project_member"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Nicholas H"}],"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"relation":"later_version","id":"11321","status":"public"},{"status":"public","id":"8254","relation":"earlier_version"}]}},{"doi":"10.15479/AT:ISTA:9949","related_material":{"record":[{"id":"10166","status":"public","relation":"used_in_publication"}]},"date_published":"2021-08-24T00:00:00Z","date_created":"2021-08-21T13:44:22Z","has_accepted_license":"1","year":"2021","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"checksum":"90461837eed66beac6fa302993cf0ca9","file_id":"9950","creator":"bvicoso","file_size":139188306,"date_updated":"2021-08-21T13:43:59Z","file_name":"Data.zip","date_created":"2021-08-21T13:43:59Z"}],"day":"24","publisher":"Institute of Science and Technology Austria","oa":1,"month":"08","oa_version":"None","author":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"article_processing_charge":"No","file_date_updated":"2021-08-21T13:43:59Z","title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","department":[{"_id":"BeVi"}],"citation":{"chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949.","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949.","mla":"Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.","short":"B. Vicoso, (2021).","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949"},"date_updated":"2024-02-21T12:40:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9949"},{"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","file":[{"file_id":"9092","checksum":"e29f2b42651bef8e034781de8781ffac","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-02-04T12:30:48Z","file_name":"2021_PlosComBio_Kavcic.pdf","creator":"dernst","date_updated":"2021-02-04T12:30:48Z","file_size":3690053}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7673","status":"public","relation":"earlier_version"},{"relation":"research_data","status":"public","id":"8930"}]},"volume":17,"abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"oa_version":"Published Version","month":"01","intvolume":" 17","date_updated":"2024-02-21T12:41:41Z","ddc":["570"],"department":[{"_id":"GaTk"}],"file_date_updated":"2021-02-04T12:30:48Z","_id":"8997","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"isi":1,"has_accepted_license":"1","year":"2021","day":"07","publication":"PLOS Computational Biology","date_published":"2021-01-07T00:00:00Z","doi":"10.1371/journal.pcbi.1008529","date_created":"2021-01-08T07:16:18Z","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008529","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"}],"article_processing_charge":"Yes","external_id":{"isi":["000608045000010"]},"title":"Minimal biophysical model of combined antibiotic action","article_number":"e1008529","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}]},{"month":"03","intvolume":" 10","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs."}],"related_material":{"record":[{"id":"8951","status":"public","relation":"research_data"}]},"volume":10,"ec_funded":1,"file":[{"creator":"bkavcic","file_size":1390469,"date_updated":"2021-03-23T10:12:58Z","file_name":"elife-65993-v2.pdf","date_created":"2021-03-23T10:12:58Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"3c2f44058c2dd45a5a1027f09d263f8e","file_id":"9284"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","status":"public","keyword":["Genetics and Molecular Biology"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9283","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2021-03-23T10:12:58Z","ddc":["570"],"date_updated":"2024-02-21T12:41:57Z","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","doi":"10.7554/elife.65993","date_published":"2021-03-08T00:00:00Z","date_created":"2021-03-23T10:11:46Z","day":"08","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2021","project":[{"call_identifier":"FP7","_id":"2517526A-B435-11E9-9278-68D0E5697425","grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies"},{"grant_number":"I03901","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks","call_identifier":"FWF","_id":"268BFA92-B435-11E9-9278-68D0E5697425"}],"article_number":"e65993","title":"Local genetic context shapes the function of a gene regulatory network","author":[{"last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A"},{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"},{"last_name":"Caruso Carter","full_name":"Caruso Carter, Caroline","first_name":"Caroline"},{"last_name":"Sonnleitner","full_name":"Sonnleitner, Elisabeth","first_name":"Elisabeth"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic"},{"full_name":"Paixão, Tiago","last_name":"Paixão","first_name":"Tiago"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"isi":["000631050900001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications, 2021, doi:10.7554/elife.65993.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993","ieee":"A. A. Nagy-Staron et al., “Local genetic context shapes the function of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021)."}},{"oa_version":"Submitted Version","abstract":[{"text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.","lang":"eng"}],"month":"12","intvolume":" 40","main_file_link":[{"open_access":"1","url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21"}],"file":[{"date_created":"2021-10-27T07:08:07Z","file_name":"rigidmolds-authorversion.pdf","creator":"bbickel","date_updated":"2021-10-27T07:08:07Z","file_size":107708317,"checksum":"384ece7a9ad1026787ba9560b04336d5","file_id":"10185","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368 "]},"publication_status":"published","issue":"6","volume":40,"ec_funded":1,"_id":"10184","status":"public","article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2024-02-28T12:52:48Z","department":[{"_id":"BeBi"}],"file_date_updated":"2021-10-27T07:08:07Z","acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"01","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-12-01T00:00:00Z","doi":"10.1145/3478513.3480555","date_created":"2021-10-27T07:08:19Z","article_number":"272","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.","mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:10.1145/3478513.3480555.","ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6). doi:10.1145/3478513.3480555","apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555","ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no. 6. Association for Computing Machinery, 2021.","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021)."},"title":"Volume decomposition for two-piece rigid casting","author":[{"first_name":"Thomas","full_name":"Alderighi, Thomas","last_name":"Alderighi"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"}],"external_id":{"isi":["000729846700077"]},"article_processing_charge":"No"},{"language":[{"iso":"eng"}],"file":[{"checksum":"a21c627683890c309a68f6389302c408","file_id":"9542","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-06-10T19:33:56Z","file_name":"MISMM-arxiv.pdf","date_updated":"2021-06-10T19:33:56Z","file_size":587404,"creator":"pdavies"}],"publication_status":"published","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"ec_funded":1,"related_material":{"record":[{"id":"7802","status":"public","relation":"earlier_version"}]},"volume":17,"issue":"2","oa_version":"Submitted Version","abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].","lang":"eng"}],"intvolume":" 17","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"ddc":["000"],"date_updated":"2024-02-28T12:53:09Z","file_date_updated":"2021-06-10T19:33:56Z","department":[{"_id":"DaAl"}],"_id":"9541","status":"public","type":"journal_article","article_type":"original","publication":"ACM Transactions on Algorithms","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-06-10T19:31:05Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1145/3451992","acknowledgement":"Institute of Science and Technology Austria (IST Austria). Email: peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick. Research partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections Grant, and EPSRC award EP/N011163/1.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 17(2), 16.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2). doi:10.1145/3451992","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing massively parallel computation with low space. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3451992","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” ACM Transactions on Algorithms, vol. 17, no. 2. Association for Computing Machinery, 2021.","short":"A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no. 2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992."},"title":"Graph sparsification for derandomizing massively parallel computation with low space","article_processing_charge":"No","external_id":{"isi":["000661311300006"],"arxiv":["1912.05390"]},"author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","last_name":"Davies"},{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"article_number":"16","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"date_created":"2021-10-13T09:21:33Z","date_published":"2021-10-12T00:00:00Z","doi":"10.1103/physrevlett.127.160602","year":"2021","isi":1,"publication":"Physical Review Letters","day":"12","oa":1,"quality_controlled":"1","publisher":"American Physical Society ","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","article_processing_charge":"No","external_id":{"isi":["000707495700001"],"arxiv":["2011.06279"]},"author":[{"first_name":"Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","last_name":"Suzuki","full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Wojciech H.","full_name":"Zurek, Wojciech H.","last_name":"Zurek"},{"last_name":"Krems","full_name":"Krems, Roman V.","first_name":"Roman V."}],"title":"Anderson localization of composite particles","citation":{"mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021, doi:10.1103/physrevlett.127.160602.","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” Physical Review Letters, vol. 127, no. 16. American Physical Society , 2021.","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson localization of composite particles. Physical Review Letters. American Physical Society . https://doi.org/10.1103/physrevlett.127.160602","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602","chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” Physical Review Letters. American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"160602","ec_funded":1,"volume":127,"issue":"16","publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2011.06279","open_access":"1"}],"scopus_import":"1","intvolume":" 127","month":"10","abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2024-02-29T12:34:10Z","type":"journal_article","article_type":"original","keyword":["General Physics and Astronomy"],"status":"public","_id":"10134"},{"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"15074"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450380706"]},"publication_status":"published","month":"07","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2005.07761","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively."}],"department":[{"_id":"DaAl"}],"date_updated":"2024-03-05T07:13:12Z","status":"public","type":"conference","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures ","end_date":"2021-07-08","location":" Virtual Event, United States","start_date":"2021-07-06"},"_id":"9678","date_published":"2021-07-06T00:00:00Z","doi":"10.1145/3409964.3461785","date_created":"2021-07-18T22:01:22Z","page":"129-139","day":"06","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","year":"2021","quality_controlled":"1","oa":1,"acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","title":"Efficient load-balancing through distributed token dropping","author":[{"full_name":"Brandt, Sebastian","last_name":"Brandt","first_name":"Sebastian"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646"},{"first_name":"Jukka","full_name":"Suomela, Jukka","last_name":"Suomela"},{"last_name":"Uitto","full_name":"Uitto, Jara","first_name":"Jara"}],"article_processing_charge":"No","external_id":{"arxiv":["2005.07761"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–39, doi:10.1145/3409964.3461785.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2021, pp. 129–139.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event, United States. https://doi.org/10.1145/3409964.3461785","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021. https://doi.org/10.1145/3409964.3461785.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139."},"project":[{"call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","name":"Coordination in constrained and natural distributed systems"}]},{"date_updated":"2024-03-05T07:35:53Z","ddc":["000"],"file_date_updated":"2021-12-27T10:36:40Z","department":[{"_id":"DaAl"}],"_id":"8286","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming ","location":"Virtual, Online; Germany","end_date":"2020-07-11","start_date":"2020-07-08"},"status":"public","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"publication_status":"published","file":[{"checksum":"21169b25b0c8e17b21e12af22bff9870","file_id":"10577","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-12-27T10:36:40Z","file_name":"2021_Algorithmica_Alistarh.pdf","creator":"cchlebak","date_updated":"2021-12-27T10:36:40Z","file_size":525950}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"15077","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. "}],"oa_version":"Published Version","scopus_import":"1","month":"12","citation":{"chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021. https://doi.org/10.1007/s00453-021-00905-9.","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2021. doi:10.1007/s00453-021-00905-9","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi"},{"first_name":"Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","full_name":"Sabour, Amirmojtaba","last_name":"Sabour"}],"external_id":{"arxiv":["2003.09297"],"isi":["000734004600001"]},"article_processing_charge":"Yes (via OA deal)","title":"Dynamic averaging load balancing on cycles","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"has_accepted_license":"1","year":"2021","day":"24","publication":"Algorithmica","date_published":"2021-12-24T00:00:00Z","doi":"10.1007/s00453-021-00905-9","date_created":"2020-08-24T06:24:04Z","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli"}],"article_processing_charge":"No","title":"The polaron at strong coupling","citation":{"mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"page":"180","date_published":"2021-08-20T00:00:00Z","doi":"10.15479/at:ista:9733","date_created":"2021-07-27T15:48:30Z","has_accepted_license":"1","year":"2021","day":"20","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"file_date_updated":"2022-03-10T12:13:57Z","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"date_updated":"2024-03-06T12:30:44Z","ddc":["515","519","539"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","_id":"9733","related_material":{"record":[{"id":"9787","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9792"},{"relation":"part_of_dissertation","status":"public","id":"9225"},{"relation":"part_of_dissertation","id":"9781","status":"public"},{"relation":"part_of_dissertation","id":"9791","status":"public"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"e88bb8ca43948abe060eb2d2fa719881","file_id":"9944","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_FeliciangeliA.pdf","date_created":"2021-08-19T14:03:48Z","creator":"dfelicia","file_size":1958710,"date_updated":"2021-09-06T09:28:56Z"},{"file_id":"9945","checksum":"72810843abee83705853505b3f8348aa","access_level":"closed","relation":"source_file","content_type":"application/octet-stream","date_created":"2021-08-19T14:06:35Z","file_name":"thesis.7z","creator":"dfelicia","date_updated":"2022-03-10T12:13:57Z","file_size":3771669}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"08","abstract":[{"text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.","lang":"eng"}],"oa_version":"Published Version"},{"_id":"9571","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2024-03-06T12:22:07Z","department":[{"_id":"DaAl"}],"file_date_updated":"2021-06-23T07:09:41Z","oa_version":"Published Version","abstract":[{"text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.","lang":"eng"}],"intvolume":" 22","month":"04","main_file_link":[{"url":"https://www.jmlr.org/papers/v22/20-255.html","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"9595","checksum":"6428aa8bcb67768b6949c99b55d5281d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-06-23T07:09:41Z","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","creator":"asandaue","date_updated":"2021-06-23T07:09:41Z","file_size":11237154}],"publication_status":"published","publication_identifier":{"eissn":["15337928"],"issn":["15324435"]},"volume":22,"issue":"114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.","ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” Journal of Machine Learning Research, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 2021;22(114):1−43.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., & Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. Journal of Machine Learning Research.","chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2021.","ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43."},"title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","article_processing_charge":"No","external_id":{"arxiv":["1908.06077"]},"author":[{"full_name":"Ramezani-Kebrya, Ali","last_name":"Ramezani-Kebrya","first_name":"Ali"},{"first_name":"Fartash","full_name":"Faghri, Fartash","last_name":"Faghri"},{"first_name":"Ilya","full_name":"Markov, Ilya","last_name":"Markov"},{"first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov","full_name":"Aksenov, Vitalii"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Roy","full_name":"Roy, Daniel M.","first_name":"Daniel M."}],"oa":1,"quality_controlled":"1","publisher":"Journal of Machine Learning Research","publication":"Journal of Machine Learning Research","day":"01","year":"2021","has_accepted_license":"1","date_created":"2021-06-20T22:01:33Z","date_published":"2021-04-01T00:00:00Z","page":"1−43"},{"title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","article_processing_charge":"No","author":[{"first_name":"Yukari H.","last_name":"Takeo","full_name":"Takeo, Yukari H."},{"last_name":"Shuster","full_name":"Shuster, S. Andrew","first_name":"S. Andrew"},{"first_name":"Linnie","full_name":"Jiang, Linnie","last_name":"Jiang"},{"full_name":"Hu, Miley","last_name":"Hu","first_name":"Miley"},{"first_name":"David J.","last_name":"Luginbuhl","full_name":"Luginbuhl, David J."},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Mark J.","last_name":"Wagner","first_name":"Mark J."},{"full_name":"Ganguli, Surya","last_name":"Ganguli","first_name":"Surya"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028","ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028","ieee":"Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028."},"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"date_created":"2020-09-21T11:59:47Z","doi":"10.1016/j.neuron.2020.11.028","date_published":"2021-02-17T00:00:00Z","page":"P629-644.E8","publication":"Neuron","day":"17","year":"2021","oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","department":[{"_id":"SiHi"}],"date_updated":"2024-03-06T12:12:48Z","status":"public","type":"journal_article","article_type":"original","_id":"8544","ec_funded":1,"volume":109,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1097-4199"]},"intvolume":" 109","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.06.14.151258"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}]},{"ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. .","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv.","apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv.","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720."},"date_updated":"2024-03-06T12:30:45Z","title":"The effective mass problem for the Landau-Pekar equations","department":[{"_id":"RoSe"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.03720"]},"author":[{"last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"article_number":"2107.03720 ","_id":"9791","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"preprint","publication":"arXiv","language":[{"iso":"eng"}],"day":"08","publication_status":"submitted","year":"2021","ec_funded":1,"date_created":"2021-08-06T08:49:45Z","date_published":"2021-07-08T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"10755","status":"public"},{"relation":"dissertation_contains","status":"public","id":"9733"}]},"acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","oa_version":"Preprint","abstract":[{"text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.","lang":"eng"}],"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/2107.03720","open_access":"1"}],"oa":1},{"oa":1,"publisher":"Cell Press","quality_controlled":"1","acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","page":"1227-1241.e5","date_created":"2020-02-28T11:00:12Z","date_published":"2021-04-07T00:00:00Z","doi":"10.1016/j.neuron.2021.01.020","year":"2021","isi":1,"publication":"Neuron","day":"07","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["000637809600006"]},"article_processing_charge":"No","author":[{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"last_name":"Hledik","full_name":"Hledik, Michal","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"title":"Statistical analysis and optimality of neural systems","citation":{"chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"scopus_import":"1","intvolume":" 109","month":"04","abstract":[{"lang":"eng","text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems."}],"oa_version":"Preprint","ec_funded":1,"volume":109,"issue":"7","related_material":{"record":[{"id":"15020","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"7553","department":[{"_id":"GaTk"}],"date_updated":"2024-03-06T14:22:51Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021.","ista":"Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405.","short":"M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405.","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. Vol 130. ML Research Press; 2021:397-405.","apa":"Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee & K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press."},"editor":[{"first_name":"Arindam","last_name":"Banerjee","full_name":"Banerjee, Arindam"},{"full_name":"Fukumizu, Kenji","last_name":"Fukumizu","first_name":"Kenji"}],"title":"Approximate message passing with spectral initialization for generalized linear models","author":[{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"first_name":"Ramji","full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan"}],"external_id":{"arxiv":["2010.03460"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"day":"01","publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","year":"2021","date_published":"2021-04-01T00:00:00Z","date_created":"2022-01-03T11:34:22Z","page":"397-405","acknowledgement":"The authors would like to thank Andrea Montanari for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.","quality_controlled":"1","publisher":"ML Research Press","oa":1,"date_updated":"2024-03-07T10:36:53Z","department":[{"_id":"MaMo"}],"_id":"10598","status":"public","type":"conference","conference":{"location":"Virtual, San Diego, CA, United States","end_date":"2021-04-15","start_date":"2021-04-13","name":"AISTATS: Artificial Intelligence and Statistics"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2640-3498"]},"publication_status":"published","volume":130,"related_material":{"record":[{"status":"public","id":"12480","relation":"later_version"}]},"oa_version":"Preprint","abstract":[{"text":" We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. ","lang":"eng"}],"month":"04","intvolume":" 130","alternative_title":["Proceedings of Machine Learning Research"],"scopus_import":"1","main_file_link":[{"url":"https://proceedings.mlr.press/v130/mondelli21a.html","open_access":"1"}]},{"publication":"Optimization and Engineering","day":"25","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2020-08-03T14:29:57Z","date_published":"2021-02-25T00:00:00Z","doi":"10.1007/s11081-020-09544-5","page":"2627-2653","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5.","ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” Optimization and Engineering, vol. 22. Springer Nature, pp. 2627–2653, 2021.","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653. doi:10.1007/s11081-020-09544-5","apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. Springer Nature. https://doi.org/10.1007/s11081-020-09544-5","chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering. Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5.","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653."},"title":"New strong convergence method for the sum of two maximal monotone operators","external_id":{"isi":["000559345400001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Qiao-Li","last_name":"Dong","full_name":"Dong, Qiao-Li"},{"first_name":"Lu-Lu","last_name":"Liu","full_name":"Liu, Lu-Lu"},{"last_name":"Yao","full_name":"Yao, Jen-Chih","first_name":"Jen-Chih"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8197","success":1,"date_updated":"2020-08-03T15:24:39Z","file_size":2137860,"creator":"dernst","date_created":"2020-08-03T15:24:39Z","file_name":"2020_OptimizationEngineering_Shehu.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1573-2924"],"issn":["1389-4420"]},"ec_funded":1,"volume":22,"oa_version":"Published Version","abstract":[{"text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.","lang":"eng"}],"intvolume":" 22","month":"02","scopus_import":"1","ddc":["510"],"date_updated":"2024-03-07T14:39:29Z","department":[{"_id":"VlKo"}],"file_date_updated":"2020-08-03T15:24:39Z","_id":"8196","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y00715","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z","ieee":"G. Scappucci et al., “The germanium quantum information route,” Nature Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.","short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z."},"title":"The germanium quantum information route","author":[{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Christoph","last_name":"Kloeffel","full_name":"Kloeffel, Christoph"},{"first_name":"Floris A.","full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg"},{"last_name":"Loss","full_name":"Loss, Daniel","first_name":"Daniel"},{"first_name":"Maksym","full_name":"Myronov, Maksym","last_name":"Myronov"},{"first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun","last_name":"Zhang"},{"first_name":"Silvano De","full_name":"Franceschi, Silvano De","last_name":"Franceschi"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"},{"last_name":"Veldhorst","full_name":"Veldhorst, Menno","first_name":"Menno"}],"external_id":{"arxiv":["2004.08133"],"isi":["000600826100003"]},"article_processing_charge":"No","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Nature Reviews Materials","isi":1,"year":"2021","date_published":"2021-10-01T00:00:00Z","doi":"10.1038/s41578-020-00262-z","date_created":"2020-12-02T10:52:51Z","page":"926–943 ","_id":"8911","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-07T14:48:57Z","department":[{"_id":"GeKa"}],"oa_version":"Preprint","abstract":[{"text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. ","lang":"eng"}],"month":"10","intvolume":" 6","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2058-8437"]},"publication_status":"published","volume":6,"ec_funded":1},{"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Discrete and Computational Geometry","day":"01","year":"2021","isi":1,"date_created":"2020-09-06T22:01:13Z","date_published":"2021-10-01T00:00:00Z","doi":"10.1007/s00454-020-00240-w","page":"938-976","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976. doi:10.1007/s00454-020-00240-w","short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 938–976, 2021.","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w."},"title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","external_id":{"isi":["000564488500002"],"arxiv":["1908.00856"]},"article_processing_charge":"No","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bobenko","full_name":"Bobenko, Alexander I.","first_name":"Alexander I."},{"last_name":"Schief","full_name":"Schief, Wolfgang K.","first_name":"Wolfgang K."},{"full_name":"Techter, Jan","last_name":"Techter","first_name":"Jan"}],"oa_version":"Preprint","abstract":[{"text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory.","lang":"eng"}],"intvolume":" 66","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1908.00856","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"ec_funded":1,"volume":66,"_id":"8338","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-03-07T14:51:11Z","department":[{"_id":"HeEd"}]},{"volume":34,"related_material":{"record":[{"id":"6933","status":"public","relation":"earlier_version"}]},"publication_status":"published","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"scopus_import":"1","intvolume":" 34","month":"12","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. "}],"oa_version":"Published Version","department":[{"_id":"DaAl"}],"date_updated":"2024-03-07T14:43:39Z","article_type":"original","type":"journal_article","status":"public","_id":"7939","page":"463-487","date_created":"2020-06-07T22:00:54Z","doi":"10.1007/s00446-020-00380-5","date_published":"2021-12-01T00:00:00Z","year":"2021","isi":1,"publication":"Distributed Computing","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","external_id":{"arxiv":["1903.05956"],"isi":["000556444600001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Keren","full_name":"Censor-Hillel, Keren","last_name":"Censor-Hillel"},{"full_name":"Dory, Michal","last_name":"Dory","first_name":"Michal"},{"first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne","last_name":"Korhonen"},{"first_name":"Dean","last_name":"Leitersdorf","full_name":"Leitersdorf, Dean"}],"title":"Fast approximate shortest paths in the congested clique","citation":{"chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing. Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87, doi:10.1007/s00446-020-00380-5.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” Distributed Computing, vol. 34. Springer Nature, pp. 463–487, 2021.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-020-00380-5","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. Distributed Computing. 2021;34:463-487. doi:10.1007/s00446-020-00380-5"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"title":"Local conditions for triangulating submanifolds of Euclidean space","author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"last_name":"Dyer","full_name":"Dyer, Ramsay","first_name":"Ramsay"},{"first_name":"Arijit","last_name":"Ghosh","full_name":"Ghosh, Arijit"},{"full_name":"Lieutier, Andre","last_name":"Lieutier","first_name":"Andre"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"external_id":{"isi":["000558119300001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686."},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"doi":"10.1007/s00454-020-00233-9","date_published":"2021-09-01T00:00:00Z","date_created":"2020-08-11T07:11:51Z","page":"666-686","day":"01","publication":"Discrete and Computational Geometry","isi":1,"has_accepted_license":"1","year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","department":[{"_id":"HeEd"}],"ddc":["510"],"date_updated":"2024-03-07T14:54:59Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8248","volume":66,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","month":"09","intvolume":" 66","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00233-9","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic.","lang":"eng"}]},{"author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"article_processing_charge":"Yes (via OA deal)","title":"Regulation of size and scale in vertebrate spinal cord development","citation":{"ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","apa":"Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. Wiley. https://doi.org/10.1002/wdev.383","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. 2021. doi:10.1002/wdev.383","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"},{"name":"Morphogen control of growth and pattern in the spinal cord","grant_number":"F07802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"article_number":"e383","date_published":"2021-04-15T00:00:00Z","doi":"10.1002/wdev.383","date_created":"2020-05-24T22:01:00Z","has_accepted_license":"1","isi":1,"year":"2021","day":"15","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","department":[{"_id":"AnKi"}],"file_date_updated":"2020-11-24T13:11:39Z","date_updated":"2024-03-07T15:03:00Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7883","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14323"}]},"ec_funded":1,"publication_identifier":{"eissn":["17597692"],"issn":["17597684"]},"publication_status":"published","file":[{"creator":"dernst","file_size":2527276,"date_updated":"2020-11-24T13:11:39Z","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","date_created":"2020-11-24T13:11:39Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8800","checksum":"f0a7745d48afa09ea7025e876a0145a8"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","abstract":[{"text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Discrete and Computational Geometry","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1007/s00454-020-00206-y","date_published":"2021-06-01T00:00:00Z","date_created":"2020-05-30T10:26:04Z","page":"1166-1198","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y.","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1166–1198, 2021.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198. doi:10.1007/s00454-020-00206-y","apa":"Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00206-y","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y."},"title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","author":[{"full_name":"Brown, Adam","last_name":"Brown","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"first_name":"Bei","full_name":"Wang, Bei","last_name":"Wang"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1712.07734"],"isi":["000536324700001"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms."}],"month":"06","intvolume":" 65","scopus_import":"1","file":[{"file_name":"2020_DiscreteCompGeometry_Brown.pdf","date_created":"2020-11-25T09:06:41Z","file_size":1013730,"date_updated":"2020-11-25T09:06:41Z","creator":"dernst","success":1,"checksum":"487a84ea5841b75f04f66d7ebd71b67e","file_id":"8803","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","volume":65,"_id":"7905","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2024-03-07T15:01:58Z","file_date_updated":"2020-11-25T09:06:41Z","department":[{"_id":"HeEd"}]},{"ec_funded":1,"publication_status":"published","publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-10-05T14:53:40Z","file_size":497032,"creator":"dernst","date_created":"2020-10-05T14:53:40Z","file_name":"2020_ProbTheory_Cipolloni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"611ae28d6055e1e298d53a57beb05ef4","file_id":"8612","success":1}],"scopus_import":"1","month":"02","abstract":[{"lang":"eng","text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble."}],"oa_version":"Published Version","department":[{"_id":"LaEr"}],"file_date_updated":"2020-10-05T14:53:40Z","date_updated":"2024-03-07T15:07:53Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8601","date_created":"2020-10-04T22:01:37Z","doi":"10.1007/s00440-020-01003-7","date_published":"2021-02-01T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"Probability Theory and Related Fields","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"title":"Edge universality for non-Hermitian random matrices","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-020-01003-7","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}]},{"scopus_import":"1","month":"09","intvolume":" 15","abstract":[{"text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method.","lang":"eng"}],"oa_version":"Published Version","volume":15,"ec_funded":1,"publication_identifier":{"issn":["1862-4472"],"eissn":["1862-4480"]},"publication_status":"published","file":[{"file_id":"15089","checksum":"63c5f31cd04626152a19f97a2476281b","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-03-07T14:58:51Z","file_name":"2021_OptimizationLetters_Shehu.pdf","date_updated":"2024-03-07T14:58:51Z","file_size":2148882,"creator":"kschuh"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7925","department":[{"_id":"VlKo"}],"file_date_updated":"2024-03-07T14:58:51Z","date_updated":"2024-03-07T15:00:43Z","ddc":["510"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","page":"2109-2126","date_published":"2021-09-01T00:00:00Z","doi":"10.1007/s11590-020-01603-1","date_created":"2020-06-04T11:28:33Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Optimization Letters","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"author":[{"orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aviv","full_name":"Gibali, Aviv","last_name":"Gibali"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000537342300001"]},"title":"New inertial relaxed method for solving split feasibilities","citation":{"short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.","ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021.","apa":"Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1","ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1","mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:10.1007/s11590-020-01603-1.","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"grant_number":"Z00312","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739","call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael"},{"first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane"},{"first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso"},{"last_name":"Suter","full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"article_processing_charge":"No","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","citation":{"ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","page":"2947–2967","doi":"10.1038/s41596-021-00526-0","date_published":"2021-06-01T00:00:00Z","date_created":"2021-05-30T22:01:24Z","has_accepted_license":"1","isi":1,"year":"2021","day":"01","publication":"Nature Protocols","article_type":"original","type":"journal_article","status":"public","_id":"9438","department":[{"_id":"PeJo"}],"file_date_updated":"2021-12-02T23:30:05Z","date_updated":"2023-08-10T22:30:51Z","ddc":["570"],"scopus_import":"1","month":"06","intvolume":" 16","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"volume":16,"issue":"6","ec_funded":1,"publication_identifier":{"issn":["17542189"],"eissn":["17502799"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9639","checksum":"7eb580abd8893cdb0b410cf41bc8c263","embargo":"2021-12-01","creator":"cziletti","date_updated":"2021-12-02T23:30:05Z","file_size":38574802,"date_created":"2021-07-08T12:27:55Z","file_name":"VandaeletalAuthorVersion2021.pdf"}],"language":[{"iso":"eng"}]},{"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"related_material":{"record":[{"status":"public","id":"6351","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6943"},{"status":"public","id":"8002","relation":"part_of_dissertation"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"checksum":"c763064adaa720e16066c1a4f9682bbb","file_id":"9993","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2021-09-09T07:29:48Z","file_name":"Thesis_vupload.docx","creator":"lhoermaye","date_updated":"2021-09-15T22:30:26Z","file_size":25179004},{"file_name":"Thesis_vfinal_pdfa.pdf","date_created":"2021-09-09T14:25:08Z","file_size":6246900,"date_updated":"2021-09-15T22:30:26Z","creator":"lhoermaye","embargo":"2021-09-09","file_id":"9996","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"_id":"9992","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2021-09-15T22:30:26Z","ddc":["575"],"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"date_updated":"2023-09-07T13:38:33Z","publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/at:ista:9992","date_published":"2021-09-13T00:00:00Z","date_created":"2021-09-09T07:37:20Z","page":"168","day":"13","has_accepted_license":"1","year":"2021","project":[{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"title":"Wound healing in the Arabidopsis root meristem","author":[{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."}},{"type":"journal_article","article_type":"original","keyword":["general medicine"],"status":"public","_id":"10816","file_date_updated":"2022-06-18T22:30:03Z","department":[{"_id":"PeJo"}],"date_updated":"2023-08-10T22:30:10Z","ddc":["610"],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/647800"}],"scopus_import":"1","intvolume":" 1","month":"12","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Submitted Version","ec_funded":1,"issue":"12","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/spot-the-difference/"}],"record":[{"id":"10110","status":"public","relation":"software"}]},"volume":1,"publication_status":"published","publication_identifier":{"issn":["2662-8457"]},"language":[{"iso":"eng"}],"file":[{"file_name":"Guzmanetal2021.pdf","date_created":"2022-06-02T12:51:07Z","creator":"patrickd","file_size":1699466,"date_updated":"2022-06-18T22:30:03Z","embargo":"2022-06-17","checksum":"9fec5b667909ef52be96d502e4f8c2ae","file_id":"11430","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"creator":"patrickd","file_size":3005651,"date_updated":"2022-06-18T22:30:03Z","file_name":"Guzmanetal2021Suppl.pdf","title":"Supplementary Material","date_created":"2022-06-02T12:53:47Z","relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf","embargo":"2022-06-17","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","file_id":"11431"}],"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"}],"article_processing_charge":"No","author":[{"full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Xiaomin","last_name":"Zhang"},{"orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","citation":{"ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","page":"830-842","date_created":"2022-03-04T08:32:36Z","doi":"10.1038/s43588-021-00157-1","date_published":"2021-12-16T00:00:00Z","year":"2021","has_accepted_license":"1","publication":"Nature Computational Science","day":"16"},{"license":"https://opensource.org/licenses/GPL-3.0","date_created":"2021-10-08T06:44:22Z","doi":"10.15479/AT:ISTA:10110","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage"}],"record":[{"relation":"used_for_analysis_in","status":"public","id":"10816"}]},"date_published":"2021-12-16T00:00:00Z","year":"2021","has_accepted_license":"1","day":"16","file":[{"success":1,"checksum":"f92f8931cad0aa7e411c1715337bf408","file_id":"10114","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"patternseparation-main (1).zip","date_created":"2021-10-08T08:46:04Z","creator":"cchlebak","file_size":332990101,"date_updated":"2021-10-08T08:46:04Z"}],"oa":1,"publisher":"IST Austria","month":"12","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"author":[{"first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","last_name":"Suter","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"file_date_updated":"2021-10-08T08:46:04Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","citation":{"chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.","mla":"Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021)."},"date_updated":"2024-03-27T23:30:11Z","ddc":["005"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","short":"GPL 3.0"},"type":"software","status":"public","_id":"10110"},{"_id":"10077","type":"preprint","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory."},"date_updated":"2024-03-27T23:30:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"}],"article_processing_charge":"No","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"month":"09","year":"2021","publication_status":"submitted","day":"29","language":[{"iso":"eng"}],"publication":"bioRxiv","related_material":{"record":[{"status":"public","id":"11932","relation":"dissertation_contains"}]},"doi":"10.1101/2021.09.28.460602","date_published":"2021-09-29T00:00:00Z","ec_funded":1,"date_created":"2021-10-04T06:23:34Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","ieee":"Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021."},"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","author":[{"first_name":"Yann K.","full_name":"Petit, Yann K.","last_name":"Petit"},{"last_name":"Mourad","full_name":"Mourad, Eléonore","first_name":"Eléonore"},{"first_name":"Christian","full_name":"Prehal, Christian","last_name":"Prehal"},{"first_name":"Christian","last_name":"Leypold","full_name":"Leypold, Christian"},{"first_name":"Andreas","full_name":"Windischbacher, Andreas","last_name":"Windischbacher"},{"last_name":"Mijailovic","full_name":"Mijailovic, Daniel","first_name":"Daniel"},{"first_name":"Christian","full_name":"Slugovc, Christian","last_name":"Slugovc"},{"first_name":"Sergey M.","full_name":"Borisov, Sergey M.","last_name":"Borisov"},{"first_name":"Egbert","full_name":"Zojer, Egbert","last_name":"Zojer"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"first_name":"Olivier","full_name":"Fontaine, Olivier","last_name":"Fontaine"},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"article_processing_charge":"No","day":"15","publication":"Nature Chemistry","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-03-15T00:00:00Z","doi":"10.1038/s41557-021-00643-z","date_created":"2021-03-16T11:12:20Z","page":"465-471","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"ddc":["540"],"date_updated":"2023-09-05T15:34:44Z","file_date_updated":"2021-09-16T22:30:03Z","department":[{"_id":"StFr"}],"_id":"9250","status":"public","keyword":["General Chemistry","General Chemical Engineering"],"article_type":"original","type":"journal_article","file":[{"creator":"dernst","date_updated":"2021-09-16T22:30:03Z","file_size":1811448,"date_created":"2021-03-22T11:46:00Z","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_id":"9276","embargo":"2021-09-15"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"publication_status":"published","issue":"5","volume":13,"pmid":1,"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"month":"03","intvolume":" 13","scopus_import":"1"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"9624","checksum":"e039225a47ef32666d59bf35ddd30ecf","creator":"scaballe","date_updated":"2022-07-02T22:30:06Z","file_size":131946790,"date_created":"2021-07-01T14:48:54Z","file_name":"PhDThesis_SCM.docx"},{"creator":"scaballe","date_updated":"2022-07-02T22:30:06Z","file_size":17094958,"date_created":"2021-07-01T14:46:25Z","file_name":"PhDThesis_SCM.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9625","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","embargo":"2022-07-01"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9750"},{"status":"public","id":"9006","relation":"part_of_dissertation"}]},"_id":"9623","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2023-09-07T13:33:27Z","ddc":["570"],"file_date_updated":"2022-07-02T22:30:06Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2021","page":"111","date_published":"2021-07-01T00:00:00Z","doi":"10.15479/at:ista:9623","date_created":"2021-07-01T14:50:17Z","citation":{"ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623","apa":"Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623","mla":"Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo"}],"article_processing_charge":"No","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002","ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002."},"title":"Cytoplasm's got moves","author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"day":"25","publication":"Developmental Cell","isi":1,"year":"2021","doi":"10.1016/j.devcel.2020.12.002","date_published":"2021-01-25T00:00:00Z","date_created":"2021-01-17T23:01:10Z","page":"P213-226","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2024-03-27T23:30:18Z","department":[{"_id":"CaHe"}],"_id":"9006","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"publication_status":"published","volume":56,"issue":"2","related_material":{"record":[{"relation":"dissertation_contains","id":"9623","status":"public"}]},"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.","lang":"eng"}],"month":"01","intvolume":" 56","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2020.12.002","open_access":"1"}]},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07807","name":"Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"3058","author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","full_name":"Morandell, Jasmin","last_name":"Morandell"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","last_name":"Tasciyan","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dimchev","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"last_name":"Dobler","full_name":"Dobler, Zoe","first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"article_processing_charge":"No","external_id":{"isi":["000658769900010"]},"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","citation":{"ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","doi":"10.1038/s41467-021-23123-x","date_published":"2021-05-24T00:00:00Z","date_created":"2021-05-28T11:49:46Z","has_accepted_license":"1","isi":1,"year":"2021","day":"24","publication":"Nature Communications","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Biochemistry","Genetics and Molecular Biology"],"_id":"9429","file_date_updated":"2021-05-28T12:39:43Z","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2024-03-27T23:30:23Z","ddc":["572"],"month":"05","intvolume":" 12","acknowledged_ssus":[{"_id":"PreCl"}],"abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"oa_version":"Published Version","volume":12,"issue":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"status":"public","id":"7800","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"12401"}]},"ec_funded":1,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9430","checksum":"337e0f7959c35ec959984cacdcb472ba","success":1,"date_updated":"2021-05-28T12:39:43Z","file_size":9358599,"creator":"kschuh","date_created":"2021-05-28T12:39:43Z","file_name":"2021_NatureCommunications_Morandell.pdf"}],"language":[{"iso":"eng"}]},{"year":"2021","has_accepted_license":"1","day":"05","page":"151","date_created":"2021-09-30T07:53:49Z","date_published":"2021-10-05T00:00:00Z","doi":"10.15479/at:ista:10058","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","project":[{"call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"djirovec","file_size":32397600,"date_updated":"2022-12-20T23:30:07Z","file_name":"PHD_Thesis_Jirovec_Source.zip","date_created":"2021-09-30T14:29:14Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","file_id":"10061"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-10-06","file_id":"10087","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_size":26910829,"date_updated":"2022-12-20T23:30:07Z","creator":"djirovec","file_name":"PHD_Thesis_pdfa2b_1.pdf","date_created":"2021-10-05T07:56:49Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8831","status":"public"},{"relation":"part_of_dissertation","id":"10065","status":"public"},{"relation":"part_of_dissertation","id":"10066","status":"public"},{"relation":"part_of_dissertation","id":"8909","status":"public"},{"status":"public","id":"5816","relation":"part_of_dissertation"}]},"abstract":[{"text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"10","date_updated":"2023-09-08T11:41:08Z","supervisor":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"ddc":["621","539"],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2022-12-20T23:30:07Z","_id":"10058","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","keyword":["qubits","quantum computing","holes"],"status":"public"},{"status":"public","article_type":"original","type":"journal_article","_id":"8909","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"date_updated":"2024-03-27T23:30:26Z","intvolume":" 20","month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"ec_funded":1,"related_material":{"record":[{"id":"9323","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"10058","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/quantum-computing-with-holes/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"8","volume":20,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"project":[{"grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"}],"title":"A singlet triplet hole spin qubit in planar Ge","article_processing_charge":"No","external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"author":[{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann","full_name":"Hofmann, Andrea C"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"first_name":"Giulio","full_name":"Tavani, Giulio","last_name":"Tavani"},{"first_name":"Marc","full_name":"Botifoll, Marc","last_name":"Botifoll"},{"orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka","full_name":"Kukucka, Josip"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi"},{"last_name":"Martins","full_name":"Martins, Frederico","orcid":"0000-0003-2668-2401","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E","first_name":"Frederico"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime"},{"orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maksim","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087","last_name":"Borovkov","full_name":"Borovkov, Maksim"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.","ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","date_created":"2020-12-02T10:50:47Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1038/s41563-021-01022-2","page":"1106–1112","publication":"Nature Materials","day":"01","year":"2021","isi":1},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"18","has_accepted_license":"1","year":"2021","date_published":"2021-05-18T00:00:00Z","doi":"10.15479/at:ista:9397","date_created":"2021-05-17T12:31:30Z","page":"101","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria."},"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","author":[{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","full_name":"Huljev, Karla"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"creator":"khuljev","file_size":47799741,"date_updated":"2022-05-21T22:30:04Z","file_name":"KHuljev_Thesis_corrections.docx","date_created":"2021-05-17T12:29:12Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398"},{"file_size":16542131,"date_updated":"2022-05-21T22:30:04Z","creator":"khuljev","file_name":"new_KHuljev_Thesis_corrections.pdf","date_created":"2021-05-18T14:50:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-05-20","file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","_id":"9397","status":"public","type":"dissertation","ddc":["571"],"supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2023-09-07T13:32:32Z","file_date_updated":"2022-05-21T22:30:04Z","department":[{"_id":"CaHe"},{"_id":"GradSch"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","ieee":"B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. .","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975","mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975."},"date_updated":"2024-03-27T23:30:26Z","department":[{"_id":"GeKa"}],"title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","author":[{"first_name":"B.","full_name":"Severin, B.","last_name":"Severin"},{"full_name":"Lennon, D. T.","last_name":"Lennon","first_name":"D. T."},{"last_name":"Camenzind","full_name":"Camenzind, L. C.","first_name":"L. C."},{"full_name":"Vigneau, F.","last_name":"Vigneau","first_name":"F."},{"full_name":"Fedele, F.","last_name":"Fedele","first_name":"F."},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"A.","last_name":"Ballabio","full_name":"Ballabio, A."},{"first_name":"D.","full_name":"Chrastina, D.","last_name":"Chrastina"},{"first_name":"G.","full_name":"Isella, G.","last_name":"Isella"},{"first_name":"M. de","full_name":"Kruijf, M. de","last_name":"Kruijf"},{"first_name":"M. J.","last_name":"Carballido","full_name":"Carballido, M. J."},{"first_name":"S.","full_name":"Svab, S.","last_name":"Svab"},{"full_name":"Kuhlmann, A. V.","last_name":"Kuhlmann","first_name":"A. V."},{"last_name":"Braakman","full_name":"Braakman, F. R.","first_name":"F. R."},{"first_name":"S.","last_name":"Geyer","full_name":"Geyer, S."},{"full_name":"Froning, F. N. M.","last_name":"Froning","first_name":"F. N. M."},{"first_name":"H.","full_name":"Moon, H.","last_name":"Moon"},{"first_name":"M. A.","full_name":"Osborne, M. A.","last_name":"Osborne"},{"first_name":"D.","last_name":"Sejdinovic","full_name":"Sejdinovic, D."},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"first_name":"D. M.","full_name":"Zumbühl, D. M.","last_name":"Zumbühl"},{"first_name":"G. A. D.","last_name":"Briggs","full_name":"Briggs, G. A. D."},{"first_name":"N.","full_name":"Ares, N.","last_name":"Ares"}],"article_processing_charge":"No","external_id":{"arxiv":["2107.12975"]},"article_number":"2107.12975","_id":"10066","project":[{"grant_number":"P30207","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","type":"preprint","day":"27","publication":"arXiv","language":[{"iso":"eng"}],"publication_status":"submitted","year":"2021","doi":"10.48550/arXiv.2107.12975","related_material":{"record":[{"relation":"dissertation_contains","id":"10058","status":"public"}]},"date_published":"2021-07-27T00:00:00Z","date_created":"2021-10-01T12:40:22Z","oa_version":"Preprint","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}],"acknowledged_ssus":[{"_id":"NanoFab"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2107.12975"}],"oa":1},{"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","date_created":"2021-05-30T22:01:23Z","doi":"10.7554/ELIFE.68274","date_published":"2021-04-29T00:00:00Z","publication":"eLife","day":"29","year":"2021","isi":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e68274","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","external_id":{"isi":["000651761700001"]},"article_processing_charge":"No","author":[{"first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","last_name":"Bhandari"},{"first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"first_name":"Diego","full_name":"Fernández-Fernández, Diego","last_name":"Fernández-Fernández"},{"first_name":"Thorsten","last_name":"Fritzius","full_name":"Fritzius, Thorsten"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","first_name":"Hüseyin C","last_name":"Önal","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Akos","full_name":"Kulik, Akos","last_name":"Kulik"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274."},"intvolume":" 10","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}],"link":[{"url":"https://doi.org/10.1101/2020.04.16.045112","relation":"earlier_version"}]},"volume":10,"language":[{"iso":"eng"}],"file":[{"checksum":"6ebcb79999f889766f7cd79ee134ad28","file_id":"9440","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-05-31T09:43:09Z","file_name":"2021_eLife_Bhandari.pdf","date_updated":"2021-05-31T09:43:09Z","file_size":8174719,"creator":"cziletti"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"9437","file_date_updated":"2021-05-31T09:43:09Z","department":[{"_id":"RySh"},{"_id":"PeJo"}],"ddc":["570"],"date_updated":"2024-03-27T23:30:30Z"},{"author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst","full_name":"Kleindienst, David"}],"article_processing_charge":"No","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","citation":{"ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"124","date_published":"2021-06-01T00:00:00Z","doi":"10.15479/at:ista:9562","date_created":"2021-06-17T14:10:47Z","has_accepted_license":"1","year":"2021","day":"01","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2022-07-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"date_updated":"2023-09-11T12:55:53Z","ddc":["570"],"type":"dissertation","status":"public","_id":"9562","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"status":"public","id":"9437","relation":"part_of_dissertation"},{"status":"public","id":"8532","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"612"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"embargo":"2022-07-01","checksum":"659df5518db495f679cb1df9e9bd1d94","file_id":"9563","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis.pdf","date_created":"2021-06-17T14:03:14Z","file_size":77299142,"date_updated":"2022-07-02T22:30:04Z","creator":"dkleindienst"},{"date_created":"2021-06-17T14:04:30Z","file_name":"Thesis_source.zip","date_updated":"2022-07-02T22:30:04Z","file_size":369804895,"creator":"dkleindienst","checksum":"3bcf63a2b19e5b6663be051bea332748","file_id":"9564","content_type":"application/zip","embargo_to":"open_access","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version"},{"month":"01","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"1386","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1437","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"relation":"part_of_dissertation","status":"public","id":"6056"},{"id":"6380","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"639","relation":"part_of_dissertation"},{"status":"public","id":"66","relation":"part_of_dissertation"},{"status":"public","id":"6780","relation":"part_of_dissertation"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7810"},{"relation":"part_of_dissertation","id":"6175","status":"public"},{"relation":"part_of_dissertation","id":"6378","status":"public"},{"relation":"part_of_dissertation","id":"6490","status":"public"},{"id":"7014","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8089"},{"status":"public","id":"8728","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7158","status":"public"},{"status":"public","id":"5977","relation":"part_of_dissertation"},{"status":"public","id":"6009","relation":"part_of_dissertation"},{"status":"public","id":"6340","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"949"}]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d1b9db3725aed34dadd81274aeb9426c","file_id":"8969","embargo":"2021-12-22","creator":"akafshda","date_updated":"2021-12-23T23:30:04Z","file_size":5251507,"date_created":"2020-12-22T20:08:44Z","file_name":"Thesis-pdfa.pdf"},{"file_size":10636756,"date_updated":"2021-03-04T23:30:04Z","creator":"akafshda","file_name":"source.zip","date_created":"2020-12-22T20:08:50Z","embargo_to":"open_access","content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"8970","checksum":"1661df7b393e6866d2460eba3c905130"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"_id":"8934","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"file_date_updated":"2021-12-23T23:30:04Z","ddc":["005"],"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"date_updated":"2023-09-22T10:03:21Z","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","date_published":"2021-01-01T00:00:00Z","doi":"10.15479/AT:ISTA:8934","date_created":"2020-12-10T12:17:07Z","page":"278","day":"01","has_accepted_license":"1","year":"2021","project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"title":"Parameterized and algebro-geometric advances in static program analysis","author":[{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021."}},{"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"related_material":{"record":[{"status":"public","id":"10316","relation":"part_of_dissertation"}]},"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10308","checksum":"b39c9e0ef18d0484d537a67551effd02","embargo":"2022-11-18","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_size":13266088,"date_created":"2021-11-18T15:07:31Z","file_name":"ThesisTomasekKathrin.pdf"},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"10309","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","creator":"ktomasek","date_updated":"2022-12-20T23:30:05Z","file_size":7539509,"date_created":"2021-11-18T15:07:46Z","file_name":"ThesisTomasekKathrin.docx"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","_id":"10307","file_date_updated":"2022-12-20T23:30:05Z","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"ddc":["570"],"supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_updated":"2023-09-07T13:34:38Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2021-11-18T00:00:00Z","doi":"10.15479/at:ista:10307","date_created":"2021-11-18T15:05:06Z","page":"73","day":"18","has_accepted_license":"1","year":"2021","title":"Pathogenic Escherichia coli hijack the host immune response","author":[{"orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."}},{"article_processing_charge":"No","author":[{"last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner"},{"id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","first_name":"Ivana","full_name":"Glatzová, Ivana","last_name":"Glatzová"},{"first_name":"Michael S.","full_name":"Lukesch, Michael S.","last_name":"Lukesch"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"citation":{"ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.).","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770.","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770."},"date_updated":"2024-03-27T23:30:35Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","status":"public","project":[{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"10316","date_created":"2021-11-19T12:24:16Z","ec_funded":1,"related_material":{"record":[{"id":"11843","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"10307"}]},"doi":"10.1101/2021.10.18.464770","date_published":"2021-10-18T00:00:00Z","publication_status":"submitted","year":"2021","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"18","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"publisher":"Cold Spring Harbor Laboratory","month":"10","abstract":[{"text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","oa_version":"Preprint"},{"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e106862","external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös"},{"first_name":"Marco","full_name":"Marconi, Marco","last_name":"Marconi"},{"first_name":"Andrea","full_name":"Vega, Andrea","last_name":"Vega"},{"first_name":"Jose","last_name":"O’Brien","full_name":"O’Brien, Jose"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia"},{"first_name":"Livio","full_name":"Antonielli, Livio","last_name":"Antonielli"},{"last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","first_name":"Juan C"},{"first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta"},{"last_name":"Artner","full_name":"Artner, Christina","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eleonore","last_name":"Bouguyon","full_name":"Bouguyon, Eleonore"},{"last_name":"Gojon","full_name":"Gojon, Alain","first_name":"Alain"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Rodrigo A.","last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A."},{"last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","citation":{"mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Embo Press","quality_controlled":"1","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","date_created":"2021-01-17T23:01:12Z","doi":"10.15252/embj.2020106862","date_published":"2021-02-01T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"EMBO Journal","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9010","file_date_updated":"2021-02-11T12:28:29Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2024-03-27T23:30:39Z","ddc":["580"],"scopus_import":"1","intvolume":" 40","month":"02","abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"volume":40,"related_material":{"record":[{"status":"public","id":"10303","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage"}]},"issue":"3","publication_status":"published","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-02-11T12:28:29Z","file_name":"2021_Embo_Otvos.pdf","date_updated":"2021-02-11T12:28:29Z","file_size":2358617,"creator":"dernst","file_id":"9110","checksum":"dc55c900f3b061d6c2790b8813d759a3","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}]},{"article_number":"e51813","citation":{"ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"author":[{"first_name":"Andrea","last_name":"Vega","full_name":"Vega, Andrea"},{"full_name":"Fredes, Isabel","last_name":"Fredes","first_name":"Isabel"},{"last_name":"O’Brien","full_name":"O’Brien, José","first_name":"José"},{"full_name":"Shen, Zhouxin","last_name":"Shen","first_name":"Zhouxin"},{"last_name":"Ötvös","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","full_name":"Abualia, Rashed","last_name":"Abualia"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A.","last_name":"Gutiérrez"}],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","oa":1,"publisher":"Wiley","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"EMBO Reports","day":"06","date_created":"2021-08-15T22:01:30Z","doi":"10.15252/embr.202051813","date_published":"2021-09-06T00:00:00Z","_id":"9913","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-27T23:30:39Z","ddc":["580"],"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"file_date_updated":"2021-10-05T13:36:42Z","abstract":[{"lang":"eng","text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 22","month":"09","publication_status":"published","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-05T13:36:42Z","file_name":"2021_EmboR_Vega.pdf","date_updated":"2021-10-05T13:36:42Z","file_size":3144854,"creator":"cchlebak","file_id":"10090","checksum":"750de03dc3b715c37090126c1548ba13","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10303","status":"public"}]},"volume":22,"issue":"9"},{"citation":{"ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","last_name":"Abualia"}],"title":"Role of hormones in nitrate regulated growth","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2021","has_accepted_license":"1","day":"22","page":"139","date_created":"2021-11-18T11:20:59Z","date_published":"2021-11-22T00:00:00Z","doi":"10.15479/at:ista:10303","_id":"10303","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","date_updated":"2023-09-19T14:42:45Z","supervisor":[{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"ddc":["580","581"],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:06Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10331","checksum":"dea38b98aa4da1cea03dcd0f10862818","embargo":"2022-11-23","date_updated":"2022-12-20T23:30:06Z","file_size":28005730,"creator":"rabualia","date_created":"2021-11-22T14:48:21Z","file_name":"AbualiaPhDthesisfinalv3.pdf"},{"checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","file_id":"10332","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"AbualiaPhDthesisfinalv3.docx","date_created":"2021-11-22T14:48:34Z","creator":"rabualia","file_size":62841883,"date_updated":"2022-12-20T23:30:06Z"}],"related_material":{"record":[{"status":"public","id":"9010","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9913"},{"relation":"part_of_dissertation","id":"47","status":"public"}]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962."},"title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"day":"02","has_accepted_license":"1","year":"2021","date_published":"2021-09-02T00:00:00Z","doi":"10.15479/at:ista:9962","date_created":"2021-08-29T12:36:50Z","page":"182","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["570"],"supervisor":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"date_updated":"2023-09-22T09:58:30Z","file_date_updated":"2022-09-03T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"_id":"9962","status":"public","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2021-08-30T09:17:39Z","file_name":"Thesis_Hansen.docx","creator":"ahansen","date_updated":"2022-09-03T22:30:04Z","file_size":10629190,"checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","file_id":"9971","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"date_updated":"2022-09-03T22:30:04Z","file_size":13457469,"creator":"ahansen","date_created":"2021-08-30T09:29:44Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9972","checksum":"204fa40321a1c6289b68c473634c4bf3","embargo":"2022-09-02"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8569"},{"relation":"part_of_dissertation","status":"public","id":"960"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration."}],"month":"09","alternative_title":["ISTA Thesis"]},{"citation":{"ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"article_processing_charge":"No","title":"Quantum many-body scars and weak breaking of ergodicity","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Nature Physics","page":"675–685","date_published":"2021-06-01T00:00:00Z","doi":"10.1038/s41567-021-01230-2","date_created":"2021-05-28T09:03:50Z","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","publisher":"Nature Research","quality_controlled":"1","oa":1,"date_updated":"2023-10-18T08:20:59Z","ddc":["539"],"department":[{"_id":"MaSe"}],"file_date_updated":"2021-12-02T23:30:03Z","_id":"9428","type":"journal_article","article_type":"review","status":"public","publication_identifier":{"eissn":["1745-2481"]},"publication_status":"published","file":[{"creator":"patrickd","date_updated":"2021-12-02T23:30:03Z","file_size":10028836,"date_created":"2021-09-20T09:27:43Z","file_name":"RevisedQMBSreview.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_id":"10026","embargo":"2021-12-01"}],"language":[{"iso":"eng"}],"volume":17,"issue":"6","ec_funded":1,"abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"oa_version":"Preprint","month":"06","intvolume":" 17"},{"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"article_number":"110750","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"author":[{"last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"first_name":"Géraldine","full_name":"Brunoud, Géraldine","last_name":"Brunoud"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc"},{"first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"last_name":"Michalko","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Milada","full_name":"Čovanová, Milada","last_name":"Čovanová"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"first_name":"Tongda","last_name":"Xu","full_name":"Xu, Tongda"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","date_created":"2020-12-09T14:48:28Z","doi":"10.1016/j.plantsci.2020.110750","date_published":"2021-02-01T00:00:00Z","publication":"Plant Science","day":"01","year":"2021","has_accepted_license":"1","isi":1,"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"8931","file_date_updated":"2021-02-04T07:49:25Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","intvolume":" 303","month":"02","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"ec_funded":1,"volume":303,"related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_PlantScience_Gelova.pdf","date_created":"2021-02-04T07:49:25Z","creator":"dernst","file_size":12563728,"date_updated":"2021-02-04T07:49:25Z","success":1,"file_id":"9083","checksum":"a7f2562bdca62d67dfa88e271b62a629","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0168-9452"]}},{"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2021","has_accepted_license":"1","isi":1,"publication":"Plant Physiology","day":"01","page":"1122–1142","date_created":"2021-03-26T12:08:38Z","date_published":"2021-06-01T00:00:00Z","doi":"10.1093/plphys/kiab134","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","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"}],"citation":{"short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","ieee":"M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"author":[{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"},{"full_name":"Himschoot, E","last_name":"Himschoot","first_name":"E"},{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Sánchez-Simarro","full_name":"Sánchez-Simarro, J","first_name":"J"},{"first_name":"F","last_name":"Aniento","full_name":"Aniento, F"},{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","abstract":[{"text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"Published Version","pmid":1,"intvolume":" 186","month":"06","publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10273","checksum":"532bb9469d3b665907f06df8c383eade","success":1,"creator":"cziletti","date_updated":"2021-11-11T15:07:51Z","file_size":2289127,"date_created":"2021-11-11T15:07:51Z","file_name":"2021_PlantPhysio_Narasimhan.pdf"}],"ec_funded":1,"related_material":{"link":[{"url":"10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"volume":186,"issue":"2","_id":"9287","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-11-11T15:07:51Z"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"month":"10","alternative_title":["ISTA Thesis"],"file":[{"embargo":"2022-10-14","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_id":"10138","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","date_created":"2021-10-14T08:00:07Z","file_size":8616142,"date_updated":"2022-12-20T23:30:03Z","creator":"cchlebak"},{"checksum":"f23ed258ca894f6aabf58b0c128bf242","file_id":"10139","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","date_created":"2021-10-14T08:00:13Z","file_size":15058499,"date_updated":"2022-12-20T23:30:03Z","creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"442","status":"public"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9287","status":"public"},{"relation":"part_of_dissertation","id":"8283","status":"public"},{"relation":"part_of_dissertation","id":"8986","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6627"},{"status":"public","id":"10095","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10015","status":"public"}]},"ec_funded":1,"_id":"10083","status":"public","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"ddc":["575"],"supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2023-10-31T19:30:02Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-12-20T23:30:03Z","publisher":"Institute of Science and Technology Austria","oa":1,"day":"06","has_accepted_license":"1","year":"2021","doi":"10.15479/at:ista:10083","date_published":"2021-10-06T00:00:00Z","date_created":"2021-10-04T13:33:10Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083."},"title":"Rapid cell growth regulation in Arabidopsis","author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"}],"article_processing_charge":"No"},{"citation":{"chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665.","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ieee":"N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021.","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. MDPI. https://doi.org/10.3390/cells10071665"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"article_processing_charge":"Yes","author":[{"full_name":"Nikonorova, N","last_name":"Nikonorova","first_name":"N"},{"first_name":"E","last_name":"Murphy","full_name":"Murphy, E"},{"first_name":"CF","last_name":"Fonseca de Lima","full_name":"Fonseca de Lima, CF"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"first_name":"B","full_name":"van de Cotte, B","last_name":"van de Cotte"},{"first_name":"LD","last_name":"Vu","full_name":"Vu, LD"},{"first_name":"D","full_name":"Balcerowicz, D","last_name":"Balcerowicz"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kong, X","last_name":"Kong","first_name":"X"},{"full_name":"De Rop, G","last_name":"De Rop","first_name":"G"},{"last_name":"Beeckman","full_name":"Beeckman, T","first_name":"T"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"K","last_name":"Vissenberg","full_name":"Vissenberg, K"},{"first_name":"PC","last_name":"Morris","full_name":"Morris, PC"},{"last_name":"Ding","full_name":"Ding, Z","first_name":"Z"},{"last_name":"De Smet","full_name":"De Smet, I","first_name":"I"}],"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","article_number":"1665 ","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"year":"2021","has_accepted_license":"1","isi":1,"publication":"Cells","day":"02","date_created":"2021-09-14T11:36:20Z","date_published":"2021-07-02T00:00:00Z","doi":"10.3390/cells10071665","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","oa":1,"publisher":"MDPI","quality_controlled":"1","date_updated":"2024-03-27T23:30:43Z","ddc":["575"],"file_date_updated":"2021-09-16T09:07:06Z","department":[{"_id":"JiFr"}],"_id":"10015","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"status":"public","publication_status":"published","publication_identifier":{"issn":["2073-4409"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-16T09:07:06Z","file_name":"2021_Cells_Nikonorova.pdf","date_updated":"2021-09-16T09:07:06Z","file_size":2667848,"creator":"cchlebak","file_id":"10021","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"volume":10,"related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"abstract":[{"lang":"eng","text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip."}],"pmid":1,"oa_version":"Published Version","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"intvolume":" 10","month":"07"},{"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"date_updated":"2024-03-27T23:30:43Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"preprint","_id":"10095","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"10223","status":"public"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"accepted","publication_identifier":{"issn":["2693-5015"]},"month":"09","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","article_processing_charge":"No","author":[{"last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Chen","full_name":"Chen, Jian","first_name":"Jian"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Sergey","last_name":"Shabala","full_name":"Shabala, Sergey"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"article_number":"266395","date_created":"2021-10-06T08:56:22Z","date_published":"2021-09-09T00:00:00Z","doi":"10.21203/rs.3.rs-266395/v3","publication":"Research Square","day":"09","year":"2021","oa":1,"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C."},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2021-11-15T17:12:57Z","date_published":"2021-11-17T00:00:00Z","doi":"10.15479/at:ista:10293","page":"171","day":"17","year":"2021","has_accepted_license":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","article_processing_charge":"No","author":[{"first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021.","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293."},"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient.","lang":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"9997","status":"public","relation":"part_of_dissertation"},{"id":"2","status":"public","relation":"part_of_dissertation"},{"id":"9402","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2022-12-20T23:30:08Z","file_size":29703124,"creator":"lschmid","date_created":"2021-11-18T12:41:46Z","file_name":"submission_new.zip","content_type":"application/zip","embargo_to":"open_access","access_level":"closed","relation":"source_file","file_id":"10305","checksum":"86a05b430756ca12ae8107b6e6f3c1e5"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2022-10-18","file_id":"10306","checksum":"d940af042e94660c6b6a7b4f0b184d47","file_size":8320985,"date_updated":"2022-12-20T23:30:08Z","creator":"lschmid","file_name":"thesis_new_upload.pdf","date_created":"2021-11-18T12:59:15Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"status":"public","type":"dissertation","_id":"10293","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"file_date_updated":"2022-12-20T23:30:08Z","ddc":["519","576"],"date_updated":"2023-11-07T08:28:29Z","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"month":"08","intvolume":" 11","file":[{"file_name":"2021_ScientificReports_Schmid.pdf","date_created":"2021-09-13T10:31:21Z","file_size":2424943,"date_updated":"2021-09-13T10:31:21Z","creator":"cchlebak","success":1,"file_id":"10006","checksum":"19df8816cf958b272b85841565c73182","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","volume":11,"related_material":{"record":[{"status":"public","id":"10293","relation":"dissertation_contains"}]},"issue":"1","ec_funded":1,"_id":"9997","status":"public","keyword":["Multidisciplinary"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["003"],"date_updated":"2024-03-27T23:30:44Z","file_date_updated":"2021-09-13T10:31:21Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"31","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.1038/s41598-021-96932-1","date_published":"2021-08-31T00:00:00Z","date_created":"2021-09-11T16:22:02Z","article_number":"17443","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1.","apa":"Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021)."},"title":"The evolution of indirect reciprocity under action and assessment generosity","author":[{"full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"full_name":"Shati, Pouya","last_name":"Shati","first_name":"Pouya"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"article_processing_charge":"Yes"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","date_created":"2021-05-18T16:56:57Z","doi":"10.1038/s41562-021-01114-8","date_published":"2021-05-13T00:00:00Z","page":"1292–1302","publication":"Nature Human Behaviour","day":"13","year":"2021","isi":1,"has_accepted_license":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"A unified framework of direct and indirect reciprocity","external_id":{"isi":["000650304000002"],"pmid":["33986519"]},"article_processing_charge":"No","author":[{"last_name":"Schmid","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8.","apa":"Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302."},"intvolume":" 5","month":"05","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability."}],"ec_funded":1,"issue":"10","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage"}]},"volume":5,"language":[{"iso":"eng"}],"file":[{"checksum":"34f55e173f90dc1dab731063458ac780","file_id":"14496","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-11-07T08:27:23Z","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","date_updated":"2023-11-07T08:27:23Z","file_size":5232761,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["2397-3374"]},"status":"public","article_type":"original","type":"journal_article","_id":"9402","file_date_updated":"2023-11-07T08:27:23Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"ddc":["000"],"date_updated":"2024-03-27T23:30:44Z"},{"author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian","last_name":"Hafner"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"article_processing_charge":"No","external_id":{"isi":["000674930900091"]},"title":"The design space of plane elastic curves","citation":{"ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","ama":"Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800","apa":"Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"article_number":"126","doi":"10.1145/3450626.3459800","date_published":"2021-07-19T00:00:00Z","date_created":"2021-08-08T22:01:26Z","isi":1,"has_accepted_license":"1","year":"2021","day":"19","publication":"ACM Transactions on Graphics","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","file_date_updated":"2021-10-18T10:42:22Z","department":[{"_id":"BeBi"}],"date_updated":"2024-03-27T23:30:45Z","ddc":["516"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2021-08-09","end_date":"2021-08-13","location":"Virtual","name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques"},"status":"public","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"_id":"9817","issue":"4","related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","relation":"press_release","description":"News on IST Website"}]},"volume":40,"ec_funded":1,"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication_status":"published","file":[{"file_size":17064290,"date_updated":"2021-10-18T10:42:15Z","creator":"chafner","file_name":"elastic-curves-paper.pdf","date_created":"2021-10-18T10:42:15Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","file_id":"10150"},{"date_created":"2021-10-18T10:42:22Z","file_name":"elastic-curves-supp.pdf","date_updated":"2021-10-18T10:42:22Z","file_size":547156,"creator":"chafner","checksum":"0088643478be7c01a703b5b10767348f","file_id":"10151","content_type":"application/pdf","access_level":"open_access","relation":"supplementary_material"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 40","abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"oa_version":"Published Version"},{"_id":"10135","status":"public","type":"dissertation","ddc":["570"],"date_updated":"2024-01-25T10:53:29Z","supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file_date_updated":"2022-12-20T23:30:05Z","oa_version":"Published Version","abstract":[{"text":"Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.","lang":"eng"}],"month":"10","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_id":"10186","checksum":"ce7108853e6cec6224f17cd6429b51fe","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","date_created":"2021-10-27T07:45:37Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx","date_updated":"2022-12-20T23:30:05Z","file_size":28508629,"creator":"cziletti"},{"checksum":"0d7afb846e8e31ec794de47bf44e12ef","file_id":"10187","embargo":"2022-10-28","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-27T07:45:57Z","file_name":"Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf","date_updated":"2022-12-20T23:30:05Z","file_size":10623525,"creator":"cziletti"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-014-5"],"issn":["2663-337X"]},"related_material":{"record":[{"id":"9160","status":"public","relation":"part_of_dissertation"}]},"project":[{"grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135.","ista":"Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria.","mla":"Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135.","short":"H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021.","ieee":"H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021.","apa":"Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135","ama":"Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135"},"title":"Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis","article_processing_charge":"No","author":[{"full_name":"Semerádová, Hana","last_name":"Semerádová","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"13","year":"2021","has_accepted_license":"1","date_created":"2021-10-13T13:42:48Z","doi":"10.15479/at:ista:10135","date_published":"2021-10-13T00:00:00Z"},{"author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal","last_name":"Agrawal","full_name":"Agrawal, Nishchal"}],"article_processing_charge":"No","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","citation":{"ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728","apa":"Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"page":"118","doi":"10.15479/at:ista:9728","date_published":"2021-07-29T00:00:00Z","date_created":"2021-07-27T13:40:30Z","has_accepted_license":"1","year":"2021","day":"29","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"_id":"9728","file_date_updated":"2022-07-29T22:30:05Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"date_updated":"2024-02-28T13:14:39Z","ddc":["532"],"alternative_title":["ISTA Thesis"],"month":"07","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"6189","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"9744","checksum":"77436be3563a90435024307b1b5ee7e8","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","date_created":"2021-07-28T13:32:02Z","creator":"nagrawal","file_size":22859658,"date_updated":"2022-07-29T22:30:05Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2022-07-28","checksum":"72a891d7daba85445c29b868c22575ed","file_id":"9745","creator":"nagrawal","file_size":18658048,"date_updated":"2022-07-29T22:30:05Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","date_created":"2021-07-28T13:32:05Z"}],"language":[{"iso":"eng"}]},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–93.","ama":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: Proceedings of the 37th International Conference on Machine Learning. PMLR. ; 2020:4082-4093.","apa":"Hasani, R., Lechner, M., Amini, A., Rus, D., & Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In Proceedings of the 37th International Conference on Machine Learning (pp. 4082–4093). Virtual.","short":"R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–4093.","ieee":"R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, pp. 4082–4093.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” In Proceedings of the 37th International Conference on Machine Learning, 4082–93. PMLR, 2020.","ista":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. Proceedings of the 37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR, , 4082–4093."},"title":"A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits","author":[{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"article_processing_charge":"No","acknowledgement":"RH and RG are partially supported by Horizon-2020 ECSEL Project grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award). AA is supported by the National Science Foundation (NSF) Graduate Research Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation of RH.\r\n","quality_controlled":"1","oa":1,"publication":"Proceedings of the 37th International Conference on Machine Learning","has_accepted_license":"1","year":"2020","date_published":"2020-01-01T00:00:00Z","date_created":"2022-01-25T15:50:34Z","page":"4082-4093","_id":"10673","series_title":"PMLR","status":"public","type":"conference","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"conference":{"name":"ML: Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-12"},"ddc":["000"],"date_updated":"2022-01-26T11:14:27Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2022-01-26T11:08:51Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level."}],"alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"url":"http://proceedings.mlr.press/v119/hasani20a.html","open_access":"1"}],"file":[{"creator":"cchlebak","date_updated":"2022-01-26T11:08:51Z","file_size":2329798,"date_created":"2022-01-26T11:08:51Z","file_name":"2020_PMLR_Hasani.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10691","checksum":"c9a4a29161777fc1a89ef451c040e3b1","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2640-3498"]},"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/"},{"title":"Getting to the root of concurrent binary search tree performance","department":[{"_id":"DaAl"}],"author":[{"first_name":"Maya","full_name":"Arbel-Raviv, Maya","last_name":"Arbel-Raviv"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Morrison, Adam","last_name":"Morrison","first_name":"Adam"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"apa":"Arbel-Raviv, M., Brown, T. A., & Morrison, A. (2020). Getting to the root of concurrent binary search tree performance. In Proceedings of the 2018 USENIX Annual Technical Conference (pp. 295–306). Boston, MA, United States: USENIX Association.","ama":"Arbel-Raviv M, Brown TA, Morrison A. Getting to the root of concurrent binary search tree performance. In: Proceedings of the 2018 USENIX Annual Technical Conference. USENIX Association; 2020:295-306.","short":"M. Arbel-Raviv, T.A. Brown, A. Morrison, in:, Proceedings of the 2018 USENIX Annual Technical Conference, USENIX Association, 2020, pp. 295–306.","ieee":"M. Arbel-Raviv, T. A. Brown, and A. Morrison, “Getting to the root of concurrent binary search tree performance,” in Proceedings of the 2018 USENIX Annual Technical Conference, Boston, MA, United States, 2020, pp. 295–306.","mla":"Arbel-Raviv, Maya, et al. “Getting to the Root of Concurrent Binary Search Tree Performance.” Proceedings of the 2018 USENIX Annual Technical Conference, USENIX Association, 2020, pp. 295–306.","ista":"Arbel-Raviv M, Brown TA, Morrison A. 2020. Getting to the root of concurrent binary search tree performance. Proceedings of the 2018 USENIX Annual Technical Conference. USENIX: Annual Technical Conference, 295–306.","chicago":"Arbel-Raviv, Maya, Trevor A Brown, and Adam Morrison. “Getting to the Root of Concurrent Binary Search Tree Performance.” In Proceedings of the 2018 USENIX Annual Technical Conference, 295–306. USENIX Association, 2020."},"date_updated":"2021-01-11T15:25:48Z","status":"public","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"type":"conference","conference":{"name":"USENIX: Annual Technical Conference","end_date":"2018-07-13","location":"Boston, MA, United States","start_date":"2018-07-11"},"_id":"7272","date_published":"2020-01-01T00:00:00Z","date_created":"2020-01-14T07:27:08Z","page":"295-306","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the 2018 USENIX Annual Technical Conference","publication_identifier":{"isbn":["9781939133021"]},"year":"2020","publication_status":"published","month":"01","publisher":"USENIX Association","scopus_import":"1","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.usenix.org/system/files/conference/atc18/atc18-arbel-raviv.pdf","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple.\r\n\r\nWe focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap.","lang":"eng"}]},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2020-01-21T16:00:26Z","date_published":"2020-02-10T00:00:00Z","doi":"10.4230/LIPIcs.OPODIS.2019.21","publication":"Proceedings of the 23rd International Conference on Principles of Distributed Systems","day":"10","year":"2020","has_accepted_license":"1","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"21","title":"The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game","external_id":{"arxiv":["1906.00110"]},"article_processing_charge":"No","author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, and Stefan Schmid. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” In Proceedings of the 23rd International Conference on Principles of Distributed Systems, Vol. 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.OPODIS.2019.21.","ista":"Schmid L, Chatterjee K, Schmid S. 2020. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. Proceedings of the 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 21.","mla":"Schmid, Laura, et al. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” Proceedings of the 23rd International Conference on Principles of Distributed Systems, vol. 153, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.OPODIS.2019.21.","ama":"Schmid L, Chatterjee K, Schmid S. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In: Proceedings of the 23rd International Conference on Principles of Distributed Systems. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.OPODIS.2019.21","apa":"Schmid, L., Chatterjee, K., & Schmid, S. (2020). The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In Proceedings of the 23rd International Conference on Principles of Distributed Systems (Vol. 153). Neuchâtel, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2019.21","short":"L. Schmid, K. Chatterjee, S. Schmid, in:, Proceedings of the 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"L. Schmid, K. Chatterjee, and S. Schmid, “The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game,” in Proceedings of the 23rd International Conference on Principles of Distributed Systems, Neuchâtel, Switzerland, 2020, vol. 153."},"intvolume":" 153","month":"02","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to \"one-shot games\"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. ","lang":"eng"}],"volume":153,"language":[{"iso":"eng"}],"file":[{"checksum":"9a91916ac2c21ab42458fcda39ef0b8d","file_id":"7608","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-03-23T09:14:06Z","file_name":"2019_LIPIcS_Schmid.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:56Z","file_size":630752}],"publication_status":"published","status":"public","conference":{"location":"Neuchâtel, Switzerland","end_date":"2019-12-19","start_date":"2019-12-17","name":"OPODIS: International Conference on Principles of Distributed Systems"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"7346","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-02-23T13:05:49Z"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"date_published":"2020-01-15T00:00:00Z","doi":"10.4230/LIPIcs.CSL.2020.20","date_created":"2020-01-21T11:22:21Z","day":"15","publication":"28th EACSL Annual Conference on Computer Science Logic","has_accepted_license":"1","year":"2020","project":[{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"20","title":"Monitoring event frequencies","author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.06097"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ferrere T, Henzinger TA, Kragl B. 2020. Monitoring event frequencies. 28th EACSL Annual Conference on Computer Science Logic. CSL: Computer Science Logic, LIPIcs, vol. 152, 20.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Bernhard Kragl. “Monitoring Event Frequencies.” In 28th EACSL Annual Conference on Computer Science Logic, Vol. 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CSL.2020.20.","ama":"Ferrere T, Henzinger TA, Kragl B. Monitoring event frequencies. In: 28th EACSL Annual Conference on Computer Science Logic. Vol 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.CSL.2020.20","apa":"Ferrere, T., Henzinger, T. A., & Kragl, B. (2020). Monitoring event frequencies. In 28th EACSL Annual Conference on Computer Science Logic (Vol. 152). Barcelona, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2020.20","ieee":"T. Ferrere, T. A. Henzinger, and B. Kragl, “Monitoring event frequencies,” in 28th EACSL Annual Conference on Computer Science Logic, Barcelona, Spain, 2020, vol. 152.","short":"T. Ferrere, T.A. Henzinger, B. Kragl, in:, 28th EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Ferrere, Thomas, et al. “Monitoring Event Frequencies.” 28th EACSL Annual Conference on Computer Science Logic, vol. 152, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.CSL.2020.20."},"month":"01","intvolume":" 152","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. ","lang":"eng"}],"volume":152,"file":[{"file_size":617206,"date_updated":"2020-07-14T12:47:56Z","creator":"bkragl","file_name":"main.pdf","date_created":"2020-01-21T11:21:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b9a691d658d075c6369d3304d17fb818","file_id":"7349"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771320"]},"publication_status":"published","status":"public","type":"conference","conference":{"location":"Barcelona, Spain","end_date":"2020-01-16","start_date":"2020-01-13","name":"CSL: Computer Science Logic"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7348","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T08:13:12Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter Triangulations Have Good Quality.” Mathematics in Computer Science. Springer Nature, 2020. https://doi.org/10.1007/s11786-020-00461-5.","ista":"Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have good quality. Mathematics in Computer Science. 14, 141–176.","mla":"Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” Mathematics in Computer Science, vol. 14, Springer Nature, 2020, pp. 141–76, doi:10.1007/s11786-020-00461-5.","ama":"Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good quality. Mathematics in Computer Science. 2020;14:141-176. doi:10.1007/s11786-020-00461-5","apa":"Choudhary, A., Kachanovich, S., & Wintraecken, M. (2020). Coxeter triangulations have good quality. Mathematics in Computer Science. Springer Nature. https://doi.org/10.1007/s11786-020-00461-5","ieee":"A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations have good quality,” Mathematics in Computer Science, vol. 14. Springer Nature, pp. 141–176, 2020.","short":"A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science 14 (2020) 141–176."},"title":"Coxeter triangulations have good quality","author":[{"first_name":"Aruni","full_name":"Choudhary, Aruni","last_name":"Choudhary"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"article_processing_charge":"Yes (via OA deal)","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"day":"01","publication":"Mathematics in Computer Science","has_accepted_license":"1","year":"2020","date_published":"2020-03-01T00:00:00Z","doi":"10.1007/s11786-020-00461-5","date_created":"2020-03-05T13:30:18Z","page":"141-176","publisher":"Springer Nature","quality_controlled":"1","oa":1,"ddc":["510"],"date_updated":"2021-01-12T08:14:13Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-11-20T10:18:02Z","_id":"7567","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1d145f3ab50ccee735983cb89236e609","file_id":"8783","creator":"dernst","file_size":872275,"date_updated":"2020-11-20T10:18:02Z","file_name":"2020_MathCompScie_Choudhary.pdf","date_created":"2020-11-20T10:18:02Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1661-8270"],"eissn":["1661-8289"]},"publication_status":"published","volume":14,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space."}],"month":"03","intvolume":" 14","scopus_import":"1"},{"has_accepted_license":"1","year":"2020","day":"20","publication":"Physical Review Research","doi":"10.1103/PhysRevResearch.2.013353","date_published":"2020-03-20T00:00:00Z","date_created":"2020-03-20T15:21:10Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"citation":{"mla":"Gotfryd, Dorota, et al. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” Physical Review Research, vol. 2, no. 1, 013353, American Physical Society, 2020, doi:10.1103/PhysRevResearch.2.013353.","short":"D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical Review Research 2 (2020).","ieee":"D. Gotfryd, E. Paerschke, J. Chaloupka, A. M. Oles, and K. Wohlfeld, “How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator,” Physical Review Research, vol. 2, no. 1. American Physical Society, 2020.","ama":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. Physical Review Research. 2020;2(1). doi:10.1103/PhysRevResearch.2.013353","apa":"Gotfryd, D., Paerschke, E., Chaloupka, J., Oles, A. M., & Wohlfeld, K. (2020). How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.2.013353","chicago":"Gotfryd, Dorota, Ekaterina Paerschke, Jiri Chaloupka, Andrzej M. Oles, and Krzysztof Wohlfeld. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” Physical Review Research. American Physical Society, 2020. https://doi.org/10.1103/PhysRevResearch.2.013353.","ista":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. 2020. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. Physical Review Research. 2(1), 013353."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gotfryd, Dorota","last_name":"Gotfryd","first_name":"Dorota"},{"id":"8275014E-6063-11E9-9B7F-6338E6697425","first_name":"Ekaterina","last_name":"Paerschke","orcid":"0000-0003-0853-8182","full_name":"Paerschke, Ekaterina"},{"full_name":"Chaloupka, Jiri","last_name":"Chaloupka","first_name":"Jiri"},{"first_name":"Andrzej M.","full_name":"Oles, Andrzej M.","last_name":"Oles"},{"first_name":"Krzysztof","full_name":"Wohlfeld, Krzysztof","last_name":"Wohlfeld"}],"article_processing_charge":"No","title":"How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator","article_number":"013353","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","file":[{"checksum":"1be551fd5f5583635076017d7391ffdc","file_id":"7610","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PhysRevResearch_Gotfryd.pdf","date_created":"2020-03-23T10:18:38Z","creator":"dernst","file_size":1436735,"date_updated":"2020-07-14T12:48:00Z"}],"language":[{"iso":"eng"}],"volume":2,"issue":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"The concept of the entanglement between spin and orbital degrees of freedom plays a crucial role in our understanding of various phases and exotic ground states in a broad class of materials, including orbitally ordered materials and spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator depends on the value of the spin-orbit coupling of the relativistic origin. To this end, we numerically diagonalize a one-dimensional spin-orbital model with Kugel-Khomskii exchange interactions between spins and orbitals on different sites supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit coupling with regard to the spin-orbital exchange, the ground state to a large extent resembles the one obtained in the limit of vanishing spin-orbit coupling. On the other hand, for large spin-orbit coupling the ground state can, depending on the model parameters, either still show negligible spin-orbital entanglement or evolve to a highly spin-orbitally-entangled phase with completely distinct properties that are described by an effective XXZ model. The presented results suggest that (i) the spin-orbital entanglement may be induced by large on-site spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates; (ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as, e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground state can, in the first order of perturbation theory, be neglected."}],"oa_version":"Published Version","month":"03","intvolume":" 2","date_updated":"2021-01-12T08:14:23Z","ddc":["530"],"file_date_updated":"2020-07-14T12:48:00Z","department":[{"_id":"MiLe"}],"_id":"7594","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2020-03-22T23:00:46Z","date_published":"2020-02-01T00:00:00Z","doi":"10.4230/LIPIcs.OPODIS.2019.15","page":"15:1-15:16","publication":"23rd International Conference on Principles of Distributed Systems","day":"01","year":"2020","has_accepted_license":"1","title":"In search of the fastest concurrent union-find algorithm","article_processing_charge":"No","external_id":{"arxiv":["1911.06347"]},"author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","first_name":"Alexander"},{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alistarh, Dan-Adrian, Alexander Fedorov, and Nikita Koval. “In Search of the Fastest Concurrent Union-Find Algorithm.” In 23rd International Conference on Principles of Distributed Systems, 153:15:1-15:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15.","ista":"Alistarh D-A, Fedorov A, Koval N. 2020. In search of the fastest concurrent union-find algorithm. 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 15:1-15:16.","mla":"Alistarh, Dan-Adrian, et al. “In Search of the Fastest Concurrent Union-Find Algorithm.” 23rd International Conference on Principles of Distributed Systems, vol. 153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16, doi:10.4230/LIPIcs.OPODIS.2019.15.","apa":"Alistarh, D.-A., Fedorov, A., & Koval, N. (2020). In search of the fastest concurrent union-find algorithm. In 23rd International Conference on Principles of Distributed Systems (Vol. 153, p. 15:1-15:16). Neuchatal, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2019.15","ama":"Alistarh D-A, Fedorov A, Koval N. In search of the fastest concurrent union-find algorithm. In: 23rd International Conference on Principles of Distributed Systems. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:15:1-15:16. doi:10.4230/LIPIcs.OPODIS.2019.15","ieee":"D.-A. Alistarh, A. Fedorov, and N. Koval, “In search of the fastest concurrent union-find algorithm,” in 23rd International Conference on Principles of Distributed Systems, Neuchatal, Switzerland, 2020, vol. 153, p. 15:1-15:16.","short":"D.-A. Alistarh, A. Fedorov, N. Koval, in:, 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16."},"intvolume":" 153","month":"02","alternative_title":["LIPIcs"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Union-Find (or Disjoint-Set Union) is one of the fundamental problems in computer science; it has been well-studied from both theoretical and practical perspectives in the sequential case. Recently, there has been mounting interest in analyzing this problem in the concurrent scenario, and several asymptotically-efficient algorithms have been proposed. Yet, to date, there is very little known about the practical performance of concurrent Union-Find. This work addresses this gap. We evaluate and analyze the performance of several concurrent Union-Find algorithms and optimization strategies across a wide range of platforms (Intel, AMD, and ARM) and workloads (social, random, and road networks, as well as integrations into more complex algorithms). We first observe that, due to the limited computational cost, the number of induced cache misses is the critical determining factor for the performance of existing algorithms. We introduce new techniques to reduce this cost by storing node priorities implicitly and by using plain reads and writes in a way that does not affect the correctness of the algorithms. Finally, we show that Union-Find implementations are an interesting application for Transactional Memory (TM): one of the fastest algorithm variants we discovered is a sequential one that uses coarse-grained locking with the lock elision optimization to reduce synchronization cost and increase scalability. ","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/3.0/","volume":153,"language":[{"iso":"eng"}],"file":[{"checksum":"d66f07ecb609d9f02433e39f80a447e9","file_id":"7609","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-03-23T09:22:48Z","file_name":"2019_LIPIcs_Alistarh.pdf","date_updated":"2020-07-14T12:48:01Z","file_size":13074131,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771337"],"issn":["18688969"]},"status":"public","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"conference":{"location":"Neuchatal, Switzerland","end_date":"2019-12-19","start_date":"2019-12-17","name":"OPODIS: International Conference on Principles of Distributed Systems"},"type":"conference","_id":"7605","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","ddc":["000"],"date_updated":"2023-02-23T13:12:12Z"},{"language":[{"iso":"eng"}],"publication":"bioRxiv","day":"19","publication_status":"published","year":"2020","date_created":"2020-03-21T16:34:42Z","doi":"10.1101/791137","date_published":"2020-02-19T00:00:00Z","page":"22","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals."}],"month":"02","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:14:26Z","citation":{"mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/791137.","ieee":"Z. Wei et al., “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020).","apa":"Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020). Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/791137","ama":"Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv. 2020. doi:10.1101/791137","chicago":"Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen, Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/791137.","ista":"Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv, 10.1101/791137."},"title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","department":[{"_id":"JiFr"}],"article_processing_charge":"No","author":[{"first_name":"Zhuang","last_name":"Wei","full_name":"Wei, Zhuang"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"last_name":"Liu","full_name":"Liu, Tao","first_name":"Tao"},{"first_name":"Yuan","last_name":"Wu","full_name":"Wu, Yuan"},{"last_name":"Lei","full_name":"Lei, Ji-Gang","first_name":"Ji-Gang"},{"last_name":"Chen","full_name":"Chen, ZhengJun","first_name":"ZhengJun"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Hong-Wei","full_name":"Xue, Hong-Wei","last_name":"Xue"},{"first_name":"Kan","last_name":"Liao","full_name":"Liao, Kan"}],"_id":"7601","status":"public","type":"preprint"},{"publication_status":"published","publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7660","checksum":"4eb102304402f5c56432516b84df86d6","creator":"dernst","file_size":1556190,"date_updated":"2020-07-14T12:48:01Z","file_name":"2020_JournRoyalSociety_Larsson.pdf","date_created":"2020-04-14T12:31:16Z"}],"volume":17,"issue":"163","abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 17","month":"02","date_updated":"2021-01-12T08:14:41Z","ddc":["570"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"7651","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2020","has_accepted_license":"1","publication":"Journal of The Royal Society Interface","day":"01","date_created":"2020-04-08T15:19:17Z","doi":"10.1098/rsif.2019.0721","date_published":"2020-02-01T00:00:00Z","oa":1,"publisher":"The Royal Society","quality_controlled":"1","citation":{"chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721.","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Larsson, J.","last_name":"Larsson","first_name":"J."},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"S.","last_name":"Bengmark","full_name":"Bengmark, S."},{"full_name":"Lundh, T.","last_name":"Lundh","first_name":"T."},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"title":"A developmentally descriptive method for quantifying shape in gastropod shells","article_number":"20190721"},{"_id":"7803","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","location":"Salerno, Italy","end_date":"2020-08-07","start_date":"2020-08-03"},"type":"conference","status":"public","date_updated":"2021-01-12T08:15:37Z","ddc":["000"],"file_date_updated":"2020-10-08T08:17:36Z","department":[{"_id":"DaAl"}],"abstract":[{"lang":"eng","text":"We settle the complexity of the (Δ+1)-coloring and (Δ+1)-list coloring problems in the CONGESTED CLIQUE model by presenting a simple deterministic algorithm for both problems running in a constant number of rounds. This matches the complexity of the recent breakthrough randomized constant-round (Δ+1)-list coloring algorithm due to Chang et al. (PODC'19), and significantly improves upon the state-of-the-art O(logΔ)-round deterministic (Δ+1)-coloring bound of Parter (ICALP'18).\r\nA remarkable property of our algorithm is its simplicity. Whereas the state-of-the-art randomized algorithms for this problem are based on the quite involved local coloring algorithm of Chang et al. (STOC'18), our algorithm can be described in just a few lines. At a high level, it applies a careful derandomization of a recursive procedure which partitions the nodes and their respective palettes into separate bins. We show that after O(1) recursion steps, the remaining uncolored subgraph within each bin has linear size, and thus can be solved locally by collecting it to a single node. This algorithm can also be implemented in the Massively Parallel Computation (MPC) model provided that each machine has linear (in n, the number of nodes in the input graph) space.\r\nWe also show an extension of our algorithm to the MPC regime in which machines have sublinear space: we present the first deterministic (Δ+1)-list coloring algorithm designed for sublinear-space MPC, which runs in O(logΔ+loglogn) rounds."}],"oa_version":"Submitted Version","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"46fe4fc58a64eb04068115573f631d4c","file_id":"8624","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"ColoringArxiv.pdf","date_created":"2020-10-08T08:17:36Z","file_size":520051,"date_updated":"2020-10-08T08:17:36Z","creator":"pdavies"}],"ec_funded":1,"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Simple, deterministic, constant-round coloring in the congested clique. In Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing (pp. 309–318). Salerno, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405751","ama":"Czumaj A, Davies P, Parter M. Simple, deterministic, constant-round coloring in the congested clique. In: Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:309-318. doi:10.1145/3382734.3405751","ieee":"A. Czumaj, P. Davies, and M. Parter, “Simple, deterministic, constant-round coloring in the congested clique,” in Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Salerno, Italy, 2020, pp. 309–318.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 309–318.","mla":"Czumaj, Artur, et al. “Simple, Deterministic, Constant-Round Coloring in the Congested Clique.” Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 309–18, doi:10.1145/3382734.3405751.","ista":"Czumaj A, Davies P, Parter M. 2020. Simple, deterministic, constant-round coloring in the congested clique. Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 309–318.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Simple, Deterministic, Constant-Round Coloring in the Congested Clique.” In Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing, 309–18. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405751."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2009.06043"]},"article_processing_charge":"No","author":[{"first_name":"Artur","full_name":"Czumaj, Artur","orcid":"0000-0002-5646-9524","last_name":"Czumaj"},{"last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"title":"Simple, deterministic, constant-round coloring in the congested clique","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","year":"2020","has_accepted_license":"1","publication":"Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing","day":"01","page":"309-318","date_created":"2020-05-06T09:02:14Z","doi":"10.1145/3382734.3405751","date_published":"2020-07-01T00:00:00Z"},{"title":"Embeddability of simplicial complexes is undecidable","article_processing_charge":"No","author":[{"last_name":"Filakovský","full_name":"Filakovský, Marek","first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"},{"last_name":"Zhechev","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan Y"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Filakovský M, Wagner U, Zhechev SY. 2020. Embeddability of simplicial complexes is undecidable. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 767–785.","chicago":"Filakovský, Marek, Uli Wagner, and Stephan Y Zhechev. “Embeddability of Simplicial Complexes Is Undecidable.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2020–January:767–85. SIAM, 2020. https://doi.org/10.1137/1.9781611975994.47.","ieee":"M. Filakovský, U. Wagner, and S. Y. Zhechev, “Embeddability of simplicial complexes is undecidable,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 767–785.","short":"M. Filakovský, U. Wagner, S.Y. Zhechev, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 767–785.","apa":"Filakovský, M., Wagner, U., & Zhechev, S. Y. (2020). Embeddability of simplicial complexes is undecidable. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2020–January, pp. 767–785). Salt Lake City, UT, United States: SIAM. https://doi.org/10.1137/1.9781611975994.47","ama":"Filakovský M, Wagner U, Zhechev SY. Embeddability of simplicial complexes is undecidable. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2020-January. SIAM; 2020:767-785. doi:10.1137/1.9781611975994.47","mla":"Filakovský, Marek, et al. “Embeddability of Simplicial Complexes Is Undecidable.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2020–January, SIAM, 2020, pp. 767–85, doi:10.1137/1.9781611975994.47."},"project":[{"grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-10T22:00:48Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1137/1.9781611975994.47","page":"767-785","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","year":"2020","oa":1,"quality_controlled":"1","publisher":"SIAM","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T08:15:38Z","status":"public","conference":{"location":"Salt Lake City, UT, United States","end_date":"2020-01-08","start_date":"2020-01-05","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","_id":"7806","volume":"2020-January","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781611975994"]},"month":"01","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611975994.47","open_access":"1"}],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"We consider the following decision problem EMBEDk→d in computational topology (where k ≤ d are fixed positive integers): Given a finite simplicial complex K of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd?\r\nThe special case EMBED1→2 is graph planarity, which is decidable in linear time, as shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are known to be decidable (as well as NP-hard), and recent results of Čadek et al. in computational homotopy theory, in combination with the classical Haefliger–Weber theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial time for any fixed pair (k, d) of dimensions in the so-called metastable range .\r\nHere, by contrast, we prove that EMBEDk→d is algorithmically undecidable for almost all pairs of dimensions outside the metastable range, namely for . This almost completely resolves the decidability vs. undecidability of EMBEDk→d in higher dimensions and establishes a sharp dichotomy between polynomial-time solvability and undecidability.\r\nOur result complements (and in a wide range of dimensions strengthens) earlier results of Matoušek, Tancer, and the second author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard for all remaining pairs (k, d) outside the metastable range and satisfying d ≥ 4.","lang":"eng"}]},{"volume":5,"ec_funded":1,"file":[{"creator":"dernst","file_size":1402146,"date_updated":"2020-07-14T12:48:03Z","file_name":"2020_FrontiersEduc_Beattie.pdf","date_created":"2020-05-11T11:34:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7818","checksum":"a24ec24e38d843341ae620ec76c53688"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2504-284X"]},"publication_status":"published","month":"05","intvolume":" 5","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"text":"Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"SiHi"}],"ddc":["570"],"date_updated":"2021-01-12T08:15:42Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7814","doi":"10.3389/feduc.2020.00048","date_published":"2020-05-08T00:00:00Z","date_created":"2020-05-11T08:18:48Z","day":"08","publication":"Frontiers in Education","has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"title":"SCOPES: Sparking curiosity through Open-Source platforms in education and science","author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 5, 48.","chicago":"Beattie, Robert J, Simon Hippenmeyer, and Florian Pauler. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” Frontiers in Education. Frontiers Media, 2020. https://doi.org/10.3389/feduc.2020.00048.","short":"R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020).","ieee":"R. J. Beattie, S. Hippenmeyer, and F. Pauler, “SCOPES: Sparking curiosity through Open-Source platforms in education and science,” Frontiers in Education, vol. 5. Frontiers Media, 2020.","ama":"Beattie RJ, Hippenmeyer S, Pauler F. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 2020;5. doi:10.3389/feduc.2020.00048","apa":"Beattie, R. J., Hippenmeyer, S., & Pauler, F. (2020). SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. Frontiers Media. https://doi.org/10.3389/feduc.2020.00048","mla":"Beattie, Robert J., et al. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” Frontiers in Education, vol. 5, 48, Frontiers Media, 2020, doi:10.3389/feduc.2020.00048."},"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"article_number":"48"},{"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). The second author has been supported by the International Research Training Group IGDK 1754 “Optimization and Numerical Analysis for Partial Differential Equations with Nonsmooth Structures”, funded by the German Research Council (DFG) and the Austrian Science Fund (FWF) under grant number [W 1244-N18].","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Journal of Elliptic and Parabolic Equations","page":"529-598","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s41808-020-00068-8","date_created":"2020-05-17T22:00:45Z","project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"citation":{"ieee":"K. Fellner and M. Kniely, “Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model,” Journal of Elliptic and Parabolic Equations, vol. 6. Springer Nature, pp. 529–598, 2020.","short":"K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020) 529–598.","apa":"Fellner, K., & Kniely, M. (2020). Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. Springer Nature. https://doi.org/10.1007/s41808-020-00068-8","ama":"Fellner K, Kniely M. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 2020;6:529-598. doi:10.1007/s41808-020-00068-8","mla":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations, vol. 6, Springer Nature, 2020, pp. 529–98, doi:10.1007/s41808-020-00068-8.","ista":"Fellner K, Kniely M. 2020. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 6, 529–598.","chicago":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations. Springer Nature, 2020. https://doi.org/10.1007/s41808-020-00068-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fellner","full_name":"Fellner, Klemens","first_name":"Klemens"},{"first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael"}],"article_processing_charge":"No","title":"Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model","abstract":[{"lang":"eng","text":"In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation."}],"oa_version":"Published Version","scopus_import":"1","month":"12","intvolume":" 6","publication_identifier":{"issn":["22969020"],"eissn":["22969039"]},"publication_status":"published","file":[{"creator":"dernst","file_size":8408694,"date_updated":"2020-11-25T08:59:59Z","file_name":"2020_JourEllipticParabEquat_Fellner.pdf","date_created":"2020-11-25T08:59:59Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6bc6832caacddceee1471291e93dcf1d","file_id":"8802"}],"language":[{"iso":"eng"}],"volume":6,"_id":"7866","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2021-01-12T08:15:47Z","ddc":["510"],"file_date_updated":"2020-11-25T08:59:59Z","department":[{"_id":"JuFi"}]},{"citation":{"ieee":"S. I. Mistakidis, A. Volosniev, and P. Schmelcher, “Induced correlations between impurities in a one-dimensional quenched Bose gas,” Physical Review Research, vol. 2. American Physical Society, 2020.","short":"S.I. Mistakidis, A. Volosniev, P. Schmelcher, Physical Review Research 2 (2020).","ama":"Mistakidis SI, Volosniev A, Schmelcher P. Induced correlations between impurities in a one-dimensional quenched Bose gas. Physical Review Research. 2020;2. doi:10.1103/physrevresearch.2.023154","apa":"Mistakidis, S. I., Volosniev, A., & Schmelcher, P. (2020). Induced correlations between impurities in a one-dimensional quenched Bose gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.2.023154","mla":"Mistakidis, S. I., et al. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” Physical Review Research, vol. 2, 023154, American Physical Society, 2020, doi:10.1103/physrevresearch.2.023154.","ista":"Mistakidis SI, Volosniev A, Schmelcher P. 2020. Induced correlations between impurities in a one-dimensional quenched Bose gas. Physical Review Research. 2, 023154.","chicago":"Mistakidis, S. I., Artem Volosniev, and P. Schmelcher. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” Physical Review Research. American Physical Society, 2020. https://doi.org/10.1103/physrevresearch.2.023154."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"S. I.","last_name":"Mistakidis","full_name":"Mistakidis, S. I."},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"},{"last_name":"Schmelcher","full_name":"Schmelcher, P.","first_name":"P."}],"article_processing_charge":"No","title":"Induced correlations between impurities in a one-dimensional quenched Bose gas","article_number":"023154 ","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"has_accepted_license":"1","year":"2020","day":"11","publication":"Physical Review Research","date_published":"2020-05-11T00:00:00Z","doi":"10.1103/physrevresearch.2.023154","date_created":"2020-06-03T11:30:10Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_updated":"2023-02-23T13:20:16Z","ddc":["530"],"file_date_updated":"2020-07-14T12:48:05Z","department":[{"_id":"MiLe"}],"_id":"7919","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"checksum":"e1c362fe094d6b246b3cd4a49722e78b","file_id":"7926","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-06-04T13:51:59Z","file_name":"2020_PhysRevResearch_Mistakidis.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:05Z","file_size":1741098}],"language":[{"iso":"eng"}],"volume":2,"ec_funded":1,"abstract":[{"lang":"eng","text":"We explore the time evolution of two impurities in a trapped one-dimensional Bose gas that follows a change of the boson-impurity interaction. We study the induced impurity-impurity interactions and their effect on the quench dynamics. In particular, we report on the size of the impurity cloud, the impurity-impurity entanglement, and the impurity-impurity correlation function. The presented numerical simulations are based upon the variational multilayer multiconfiguration time-dependent Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations, we employ an effective two-body Hamiltonian with a contact interaction. We show that the effective model consistent with the mean-field attraction of two heavy impurities explains qualitatively our results for weak interactions. Our findings suggest that the quench dynamics in cold-atom systems can be a tool for studying impurity-impurity correlations."}],"oa_version":"Published Version","month":"05","intvolume":" 2"},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2020-06-22T09:14:19Z","date_published":"2020-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2020.12","year":"2020","has_accepted_license":"1","publication":"36th International Symposium on Computational Geometry","day":"01","project":[{"call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312"}],"article_number":"12:1 - 12:15","article_processing_charge":"No","external_id":{"arxiv":["1909.00263"]},"author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"},{"full_name":"Nivasch, Gabriel","last_name":"Nivasch","first_name":"Gabriel"}],"title":"Homotopic curve shortening and the affine curve-shortening flow","citation":{"mla":"Avvakumov, Sergey, and Gabriel Nivasch. “Homotopic Curve Shortening and the Affine Curve-Shortening Flow.” 36th International Symposium on Computational Geometry, vol. 164, 12:1-12:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.12.","ieee":"S. Avvakumov and G. Nivasch, “Homotopic curve shortening and the affine curve-shortening flow,” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","short":"S. Avvakumov, G. Nivasch, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ama":"Avvakumov S, Nivasch G. Homotopic curve shortening and the affine curve-shortening flow. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.12","apa":"Avvakumov, S., & Nivasch, G. (2020). Homotopic curve shortening and the affine curve-shortening flow. In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.12","chicago":"Avvakumov, Sergey, and Gabriel Nivasch. “Homotopic Curve Shortening and the Affine Curve-Shortening Flow.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.12.","ista":"Avvakumov S, Nivasch G. 2020. Homotopic curve shortening and the affine curve-shortening flow. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 12:1-12:15."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 164","month":"06","abstract":[{"lang":"eng","text":"We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between \"grid peeling\" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase."}],"oa_version":"Published Version","volume":164,"publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771436"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8007","checksum":"6872df6549142f709fb6354a1b2f2c06","creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":575896,"date_created":"2020-06-23T11:13:49Z","file_name":"2020_LIPIcsSoCG_Avvakumov.pdf"}],"conference":{"start_date":"2020-06-22","end_date":"2020-06-26","location":"Zürich, Switzerland","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"conference","status":"public","_id":"7991","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T08:16:23Z","ddc":["510"]},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"36th International Symposium on Computational Geometry","date_published":"2020-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2020.61","date_created":"2020-06-22T09:14:18Z","article_number":"61:1-61:13","citation":{"apa":"Patakova, Z. (2020). Bounding radon number via Betti numbers. In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.61","ama":"Patakova Z. Bounding radon number via Betti numbers. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.61","ieee":"Z. Patakova, “Bounding radon number via Betti numbers,” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","short":"Z. Patakova, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Patakova, Zuzana. “Bounding Radon Number via Betti Numbers.” 36th International Symposium on Computational Geometry, vol. 164, 61:1-61:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.61.","ista":"Patakova Z. 2020. Bounding radon number via Betti numbers. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 61:1-61:13.","chicago":"Patakova, Zuzana. “Bounding Radon Number via Betti Numbers.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.61."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"}],"external_id":{"arxiv":["1908.01677"]},"article_processing_charge":"No","title":"Bounding radon number via Betti numbers","abstract":[{"lang":"eng","text":"We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"month":"06","intvolume":" 164","publication_identifier":{"issn":["18688969"],"isbn":["9783959771436"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":645421,"date_created":"2020-06-23T06:56:23Z","file_name":"2020_LIPIcsSoCG_Patakova_61.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8005","checksum":"d0996ca5f6eb32ce955ce782b4f2afbe"}],"language":[{"iso":"eng"}],"volume":164,"_id":"7989","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2020-06-22","end_date":"2020-06-26","location":"Zürich, Switzerland","name":"SoCG: Symposium on Computational Geometry"},"status":"public","date_updated":"2021-01-12T08:16:22Z","ddc":["510"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z"},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"36th International Symposium on Computational Geometry","day":"01","year":"2020","has_accepted_license":"1","date_created":"2020-06-22T09:14:20Z","doi":"10.4230/LIPIcs.SoCG.2020.62","date_published":"2020-06-01T00:00:00Z","article_number":"62:1 - 62:16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Patakova, Zuzana, Martin Tancer, and Uli Wagner. “Barycentric Cuts through a Convex Body.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.62.","ista":"Patakova Z, Tancer M, Wagner U. 2020. Barycentric cuts through a convex body. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 62:1-62:16.","mla":"Patakova, Zuzana, et al. “Barycentric Cuts through a Convex Body.” 36th International Symposium on Computational Geometry, vol. 164, 62:1-62:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.62.","short":"Z. Patakova, M. Tancer, U. Wagner, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"Z. Patakova, M. Tancer, and U. Wagner, “Barycentric cuts through a convex body,” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","apa":"Patakova, Z., Tancer, M., & Wagner, U. (2020). Barycentric cuts through a convex body. In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.62","ama":"Patakova Z, Tancer M, Wagner U. Barycentric cuts through a convex body. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.62"},"title":"Barycentric cuts through a convex body","article_processing_charge":"No","external_id":{"arxiv":["2003.13536"]},"author":[{"first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683"},{"last_name":"Tancer","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3."}],"intvolume":" 164","month":"06","scopus_import":1,"alternative_title":["LIPIcs"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8004","checksum":"ce1c9194139a664fb59d1efdfc88eaae","file_size":750318,"date_updated":"2020-07-14T12:48:06Z","creator":"dernst","file_name":"2020_LIPIcsSoCG_Patakova.pdf","date_created":"2020-06-23T06:45:52Z"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771436"],"issn":["18688969"]},"volume":164,"_id":"7992","status":"public","conference":{"start_date":"2020-06-22","end_date":"2020-06-26","location":"Zürich, Switzerland","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","ddc":["510"],"date_updated":"2021-01-12T08:16:23Z","file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"UlWa"}]},{"date_updated":"2023-02-23T13:22:12Z","ddc":["510"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z","_id":"7994","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2020-06-26","location":"Zürich, Switzerland","start_date":"2020-06-22","name":"SoCG: Symposium on Computational Geometry"},"status":"public","publication_identifier":{"issn":["18688969"],"isbn":["9783959771436"]},"publication_status":"published","file":[{"file_id":"8006","checksum":"93571b76cf97d5b7c8aabaeaa694dd7e","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-06-23T11:06:23Z","file_name":"2020_LIPIcsSoCG_Arroyo.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":592661}],"language":[{"iso":"eng"}],"volume":164,"ec_funded":1,"abstract":[{"lang":"eng","text":"In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible."}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":"1","month":"06","intvolume":" 164","citation":{"apa":"Arroyo Guevara, A. M., Bensmail, J., & Bruce Richter, R. (2020). Extending drawings of graphs to arrangements of pseudolines. In 36th International Symposium on Computational Geometry (Vol. 164). Zürich, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2020.9","ama":"Arroyo Guevara AM, Bensmail J, Bruce Richter R. Extending drawings of graphs to arrangements of pseudolines. In: 36th International Symposium on Computational Geometry. Vol 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.SoCG.2020.9","short":"A.M. Arroyo Guevara, J. Bensmail, R. Bruce Richter, in:, 36th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"A. M. Arroyo Guevara, J. Bensmail, and R. Bruce Richter, “Extending drawings of graphs to arrangements of pseudolines,” in 36th International Symposium on Computational Geometry, Zürich, Switzerland, 2020, vol. 164.","mla":"Arroyo Guevara, Alan M., et al. “Extending Drawings of Graphs to Arrangements of Pseudolines.” 36th International Symposium on Computational Geometry, vol. 164, 9:1-9:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.SoCG.2020.9.","ista":"Arroyo Guevara AM, Bensmail J, Bruce Richter R. 2020. Extending drawings of graphs to arrangements of pseudolines. 36th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 164, 9:1-9:14.","chicago":"Arroyo Guevara, Alan M, Julien Bensmail, and R. Bruce Richter. “Extending Drawings of Graphs to Arrangements of Pseudolines.” In 36th International Symposium on Computational Geometry, Vol. 164. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.SoCG.2020.9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"first_name":"Julien","last_name":"Bensmail","full_name":"Bensmail, Julien"},{"first_name":"R.","last_name":"Bruce Richter","full_name":"Bruce Richter, R."}],"external_id":{"arxiv":["1804.09317"]},"article_processing_charge":"No","title":"Extending drawings of graphs to arrangements of pseudolines","article_number":"9:1 - 9:14","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2020","day":"01","publication":"36th International Symposium on Computational Geometry","date_published":"2020-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2020.9","date_created":"2020-06-22T09:14:21Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1},{"publication":"Physical Review Research","day":"22","year":"2020","has_accepted_license":"1","date_created":"2020-06-23T12:00:19Z","date_published":"2020-06-22T00:00:00Z","doi":"10.1103/physrevresearch.2.022065","oa":1,"quality_controlled":"1","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Stabilizing Two-Dimensional Quantum Scars by Deformation and Synchronization.” Physical Review Research. American Physical Society, 2020. https://doi.org/10.1103/physrevresearch.2.022065.","ista":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Stabilizing two-dimensional quantum scars by deformation and synchronization. Physical Review Research. 2(2), 022065.","mla":"Michailidis, Alexios, et al. “Stabilizing Two-Dimensional Quantum Scars by Deformation and Synchronization.” Physical Review Research, vol. 2, no. 2, 022065, American Physical Society, 2020, doi:10.1103/physrevresearch.2.022065.","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review Research 2 (2020).","ieee":"A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Stabilizing two-dimensional quantum scars by deformation and synchronization,” Physical Review Research, vol. 2, no. 2. American Physical Society, 2020.","apa":"Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., & Serbyn, M. (2020). Stabilizing two-dimensional quantum scars by deformation and synchronization. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.2.022065","ama":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Stabilizing two-dimensional quantum scars by deformation and synchronization. Physical Review Research. 2020;2(2). doi:10.1103/physrevresearch.2.022065"},"title":"Stabilizing two-dimensional quantum scars by deformation and synchronization","article_processing_charge":"No","author":[{"last_name":"Michailidis","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios"},{"first_name":"C. J.","last_name":"Turner","full_name":"Turner, C. J."},{"full_name":"Papić, Z.","last_name":"Papić","first_name":"Z."},{"full_name":"Abanin, D. A.","last_name":"Abanin","first_name":"D. A."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"article_number":"022065","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8050","checksum":"e6959dc8220f14a008d1933858795e6d","date_updated":"2020-07-14T12:48:08Z","file_size":2066011,"creator":"dernst","date_created":"2020-06-29T14:41:27Z","file_name":"2020_PhysicalReviewResearch_Michailidis.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"ec_funded":1,"issue":"2","volume":2,"oa_version":"Published Version","abstract":[{"text":"Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars.","lang":"eng"}],"intvolume":" 2","month":"06","ddc":["530"],"date_updated":"2021-01-12T08:16:30Z","department":[{"_id":"MaSe"}],"file_date_updated":"2020-07-14T12:48:08Z","_id":"8011","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"}]