[{"file":[{"content_type":"application/pdf","file_name":"2022_NatureCommunications_Radler.pdf","date_updated":"2022-05-13T09:10:51Z","file_size":6945191,"checksum":"5af863ee1b95a0710f6ee864d68dc7a6","date_created":"2022-05-13T09:10:51Z","creator":"dernst","file_id":"11374","access_level":"open_access","relation":"main_file","success":1}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}],"record":[{"status":"public","id":"14280","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"10934"}]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2041-1723"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-05-12T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"month":"05","article_number":"2635","publication":"Nature Communications","has_accepted_license":"1","volume":13,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","ddc":["570"],"doi":"10.1038/s41467-022-30301-y","day":"12","abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"date_updated":"2024-02-21T12:35:18Z","year":"2022","citation":{"short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>."},"isi":1,"external_id":{"isi":["000795171100037"]},"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-05-13T09:10:51Z","publication_status":"published","department":[{"_id":"MaLo"}],"date_created":"2022-05-13T09:06:28Z","article_processing_charge":"No","title":"In vitro reconstitution of Escherichia coli divisome activation","intvolume":"        13","_id":"11373","scopus_import":"1","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","first_name":"Philipp","last_name":"Radler"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"id":"B9577E20-AA38-11E9-AC9A-0930E6697425","full_name":"Michalik, David","last_name":"Michalik","first_name":"David"},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}]},{"oa_version":"Preprint","month":"04","publication":"Nano Letters","language":[{"iso":"eng"}],"publication_identifier":{"issn":["15306984"],"eissn":["15306992"]},"oa":1,"date_published":"2022-04-27T00:00:00Z","type":"journal_article","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.00556","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_status":"published","department":[{"_id":"MaSe"}],"date_created":"2022-05-15T22:01:41Z","article_processing_charge":"No","title":"Spontaneous gully-polarized quantum hall states in ABA trilayer graphene","intvolume":"        22","_id":"11379","scopus_import":"1","author":[{"full_name":"Winterer, Felix","first_name":"Felix","last_name":"Winterer"},{"full_name":"Seiler, Anna M.","first_name":"Anna M.","last_name":"Seiler"},{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Geisenhof","first_name":"Fabian R.","full_name":"Geisenhof, Fabian R."},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"first_name":"Takashi","last_name":"Taniguchi","full_name":"Taniguchi, Takashi"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"first_name":"R. Thomas","last_name":"Weitz","full_name":"Weitz, R. Thomas"}],"issue":"8","publisher":"American Chemical Society","article_type":"original","page":"3317-3322","quality_controlled":"1","doi":"10.1021/acs.nanolett.2c00435","arxiv":1,"day":"27","abstract":[{"text":"Bernal-stacked multilayer graphene is a versatile platform to explore quantum transport phenomena and interaction physics due to its exceptional tunability via electrostatic gating. For instance, upon applying a perpendicular electric field, its band structure exhibits several off-center Dirac points (so-called Dirac gullies) in each valley. Here, the formation of Dirac gullies and the interaction-induced breakdown of gully coherence is explored via magnetotransport measurements in high-quality Bernal-stacked (ABA) trilayer graphene. At zero magnetic field, multiple Lifshitz transitions indicating the formation of Dirac gullies are identified. In the quantum Hall regime, the emergence of Dirac gullies is evident as an increase in Landau level degeneracy. When tuning both electric and magnetic fields, electron–electron interactions can be controllably enhanced until, beyond critical electric and magnetic fields, the gully degeneracy is eventually lifted. The arising correlated ground state is consistent with a previously predicted nematic phase that spontaneously breaks the rotational gully symmetry.","lang":"eng"}],"date_updated":"2023-08-03T07:12:45Z","year":"2022","citation":{"short":"F. Winterer, A.M. Seiler, A. Ghazaryan, F.R. Geisenhof, K. Watanabe, T. Taniguchi, M. Serbyn, R.T. Weitz, Nano Letters 22 (2022) 3317–3322.","mla":"Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” <i>Nano Letters</i>, vol. 22, no. 8, American Chemical Society, 2022, pp. 3317–22, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>.","ista":"Winterer F, Seiler AM, Ghazaryan A, Geisenhof FR, Watanabe K, Taniguchi T, Serbyn M, Weitz RT. 2022. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. Nano Letters. 22(8), 3317–3322.","ama":"Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. <i>Nano Letters</i>. 2022;22(8):3317-3322. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>","apa":"Winterer, F., Seiler, A. M., Ghazaryan, A., Geisenhof, F. R., Watanabe, K., Taniguchi, T., … Weitz, R. T. (2022). Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>","ieee":"F. Winterer <i>et al.</i>, “Spontaneous gully-polarized quantum hall states in ABA trilayer graphene,” <i>Nano Letters</i>, vol. 22, no. 8. American Chemical Society, pp. 3317–3322, 2022.","chicago":"Winterer, Felix, Anna M. Seiler, Areg Ghazaryan, Fabian R. Geisenhof, Kenji Watanabe, Takashi Taniguchi, Maksym Serbyn, and R. Thomas Weitz. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” <i>Nano Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>."},"isi":1,"external_id":{"arxiv":["2109.00556"],"isi":["000809056900019"]},"acknowledgement":"We acknowledge funding from the Center for Nanoscience (CeNS) and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy-EXC-2111-390814868 (MCQST). K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan (Grant Number PMXP0112101001) and JSPS KAKENHI (Grant Numbers 19H05790 and JP20H00354).","volume":22},{"_id":"11388","author":[{"orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-05-16T16:49:18Z","publication_status":"published","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","alternative_title":["ISTA Thesis"],"page":"98","file_date_updated":"2023-05-20T22:30:03Z","publisher":"Institute of Science and Technology Austria","year":"2022","citation":{"mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>."},"date_updated":"2023-08-29T06:41:51Z","day":"18","doi":"10.15479/at:ista:11388","degree_awarded":"PhD","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"ddc":["576"],"has_accepted_license":"1","oa_version":"Published Version","month":"05","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"dissertation","date_published":"2022-05-18T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-018-3"]},"oa":1,"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"sbelohla","file_id":"11398","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"thesis_sb_final_pdfa.pdf","date_updated":"2023-05-20T22:30:03Z","file_size":8247240,"checksum":"4d75e6a619df7e8a9d6e840aee182380","date_created":"2022-05-19T13:03:13Z","embargo":"2023-05-19"},{"embargo_to":"open_access","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","file_size":7094,"date_created":"2022-05-19T13:07:47Z","content_type":"application/x-zip-compressed","file_name":"thesis_sb_final.zip","date_updated":"2023-05-20T22:30:03Z","access_level":"closed","relation":"source_file","creator":"sbelohla","file_id":"11399"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"6713","relation":"part_of_dissertation","status":"public"}]}},{"page":"108","file_date_updated":"2023-05-17T22:30:03Z","publisher":"Institute of Science and Technology Austria","_id":"11393","author":[{"first_name":"Marijo","last_name":"Jevtic","full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-05-17T08:57:41Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","ddc":["570"],"citation":{"ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria."},"year":"2022","date_updated":"2023-09-07T14:53:44Z","day":"16","degree_awarded":"PhD","doi":"10.15479/at:ista:11393","abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"05","file":[{"file_id":"11395","creator":"cchlebak","access_level":"closed","relation":"source_file","date_updated":"2023-05-17T22:30:03Z","file_name":"MJ thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-05-17T09:08:06Z","checksum":"8fc695d88020d70d231dad0e9f10b138","file_size":56427603,"embargo_to":"open_access"},{"relation":"main_file","access_level":"open_access","creator":"cchlebak","file_id":"11397","file_size":4351981,"checksum":"c1dd20a1aece521b3500607b00e463d6","date_created":"2022-05-17T12:09:25Z","embargo":"2023-05-16","file_name":"MJ_thesis_PDFA.pdf","content_type":"application/pdf","date_updated":"2023-05-17T22:30:03Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7391"}]},"type":"dissertation","date_published":"2022-05-16T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}]},{"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"The Journal of Chemical Physics","article_number":"194902","month":"05","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"oa_version":"Published Version","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","file_id":"11405","success":1,"relation":"main_file","access_level":"open_access","file_name":"2022_JourChemPhysics_Palaia.pdf","content_type":"application/pdf","date_updated":"2022-05-23T07:45:33Z","file_size":6387208,"checksum":"7fada58059676a4bb0944b82247af740","date_created":"2022-05-23T07:45:33Z"}],"type":"journal_article","date_published":"2022-05-16T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"file_date_updated":"2022-05-23T07:45:33Z","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"AIP Publishing","issue":"19","author":[{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","first_name":"Ivan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"}],"_id":"11400","intvolume":"       156","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","article_processing_charge":"No","department":[{"_id":"AnSa"}],"date_created":"2022-05-22T17:04:48Z","publication_status":"published","ddc":["540"],"volume":156,"acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","external_id":{"isi":["000797236000004"]},"isi":1,"year":"2022","citation":{"short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>."},"date_updated":"2023-09-05T11:59:00Z","abstract":[{"lang":"eng","text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes."}],"day":"16","doi":"10.1063/5.0087769"},{"quality_controlled":"1","file_date_updated":"2022-05-23T06:47:57Z","publisher":"Springer Nature","article_type":"original","_id":"11401","scopus_import":"1","author":[{"full_name":"Nguyen, Van Quang","first_name":"Van Quang","last_name":"Nguyen"},{"last_name":"Trinh","first_name":"Thi Ly","full_name":"Trinh, Thi Ly"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"},{"last_name":"Nguyen","first_name":"Thi Huong","full_name":"Nguyen, Thi Huong"},{"first_name":"Van Thiet","last_name":"Duong","full_name":"Duong, Van Thiet"},{"full_name":"Duong, Anh Tuan","first_name":"Anh Tuan","last_name":"Duong"},{"last_name":"Park","first_name":"Jong Ho","full_name":"Park, Jong Ho"},{"full_name":"Park, Sudong","last_name":"Park","first_name":"Sudong"},{"last_name":"Kim","first_name":"Jungdae","full_name":"Kim, Jungdae"},{"last_name":"Cho","first_name":"Sunglae","full_name":"Cho, Sunglae"}],"publication_status":"published","article_processing_charge":"No","date_created":"2022-05-22T22:01:40Z","department":[{"_id":"MaIb"}],"title":"Unidentified major p-type source in SnSe: Multivacancies","intvolume":"        14","acknowledgement":"This work was supported by the National Research Foundation of Korea [NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].","volume":14,"ddc":["540"],"date_updated":"2023-08-03T07:13:58Z","year":"2022","citation":{"chicago":"Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>.","ieee":"V. Q. Nguyen <i>et al.</i>, “Unidentified major p-type source in SnSe: Multivacancies,” <i>NPG Asia Materials</i>, vol. 14. Springer Nature, 2022.","ama":"Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. 2022;14. doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>","apa":"Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong, V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>","ista":"Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies. NPG Asia Materials. 14, 42.","short":"V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T. Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022).","mla":"Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>, vol. 14, 42, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>."},"isi":1,"external_id":{"isi":["000794880200001"]},"doi":"10.1038/s41427-022-00393-5","day":"13","abstract":[{"text":"Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower group dopants to achieve successful p-type doping in SnSe with high ZT values. A known, facile, and powerful alternative way to introduce a hole carrier is to use a natural single Sn vacancy, VSn. Through transport and scanning tunneling microscopy studies, we discovered that VSn are dominant in high-quality (slow cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and Vmulti help to increase the power factors of SnSe, whereas samples with dominant VSn have superior thermoelectric properties in SnSe single crystals. Additionally, the observation that Vmulti are good p-type sources observed in relatively low-quality single crystals is useful in thermoelectric applications because polycrystalline SnSe can be used due to its mechanical strength; this substance is usually fabricated at very high cooling speeds.","lang":"eng"}],"language":[{"iso":"eng"}],"publication":"NPG Asia Materials","has_accepted_license":"1","oa_version":"Published Version","month":"05","article_number":"42","file":[{"date_created":"2022-05-23T06:47:57Z","file_size":6202545,"checksum":"0579997cc1d28bf66e29357e08e3e39d","date_updated":"2022-05-23T06:47:57Z","content_type":"application/pdf","file_name":"2022_NPGAsiaMaterials_Nguyen.pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"11404","creator":"dernst"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-05-13T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1884-4049"],"eissn":["1884-4057"]},"oa":1},{"abstract":[{"lang":"eng","text":"Fixed-horizon planning considers a weighted graph and asks to construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping-time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary as the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping-time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time."}],"day":"01","arxiv":1,"doi":"10.1016/j.jcss.2022.04.003","external_id":{"isi":["000805002800001"],"arxiv":["1802.03642"]},"isi":1,"citation":{"ista":"Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon. Journal of Computer and System Sciences. 129, 1–21.","short":"K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022) 1–21.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>, vol. 129, Elsevier, 2022, pp. 1–21, doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” <i>Journal of Computer and System Sciences</i>, vol. 129. Elsevier, pp. 1–21, 2022.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2022). Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. 2022;129:1-21. doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>"},"year":"2022","date_updated":"2025-07-14T09:09:54Z","acknowledgement":"This work was partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).","volume":129,"intvolume":"       129","title":"Graph planning with expected finite horizon","date_created":"2022-05-22T22:01:40Z","department":[{"_id":"KrCh"}],"article_processing_charge":"No","publication_status":"published","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"scopus_import":"1","_id":"11402","article_type":"original","publisher":"Elsevier","ec_funded":1,"quality_controlled":"1","page":"1-21","oa":1,"publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"type":"journal_article","date_published":"2022-11-01T00:00:00Z","related_material":{"record":[{"id":"7402","relation":"earlier_version","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1802.03642","open_access":"1"}],"month":"11","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Preprint","publication":"Journal of Computer and System Sciences","language":[{"iso":"eng"}]},{"volume":3,"citation":{"mla":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6, Springer Nature, 2022, p. 360, doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>.","short":"A. Stöllner, Nature Reviews Earth and Environment 3 (2022) 360.","ista":"Stöllner A. 2022. Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. 3(6), 360.","ama":"Stöllner A. Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. 2022;3(6):360. doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>","apa":"Stöllner, A. (2022). Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>","ieee":"A. Stöllner, “Measuring airborne nanoplastics using aerosol physics,” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6. Springer Nature, p. 360, 2022.","chicago":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>."},"year":"2022","date_updated":"2023-11-28T09:53:42Z","external_id":{"isi":["000791125600002"]},"isi":1,"day":"01","doi":"10.1038/s43017-022-00302-y","quality_controlled":"1","page":"360","publisher":"Springer Nature","article_type":"original","scopus_import":"1","_id":"11403","issue":"6","author":[{"id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","full_name":"Stöllner, Andrea","orcid":"0000-0002-0464-8440","last_name":"Stöllner","first_name":"Andrea"}],"date_created":"2022-05-22T22:01:41Z","article_processing_charge":"No","department":[{"_id":"GradSch"}],"publication_status":"published","intvolume":"         3","title":"Measuring airborne nanoplastics using aerosol physics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","date_published":"2022-06-01T00:00:00Z","publication_identifier":{"eissn":["2662-138X"]},"language":[{"iso":"eng"}],"publication":"Nature Reviews Earth and Environment","oa_version":"None","month":"06"},{"date_created":"2022-05-26T13:44:50Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","publication_status":"published","intvolume":"       221","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","scopus_import":"1","_id":"11411","pmid":1,"issue":"3","author":[{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publisher":"Oxford University Press","article_type":"original","quality_controlled":"1","file_date_updated":"2022-05-26T12:48:21Z","day":"01","doi":"10.1093/genetics/iyac083","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"citation":{"ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022)."},"year":"2022","date_updated":"2024-02-21T12:38:33Z","external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"isi":1,"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","volume":221,"ddc":["576"],"project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","article_number":"iyac083","month":"07","has_accepted_license":"1","publication":"Genetics","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1943-2631"]},"oa":1,"type":"journal_article","date_published":"2022-07-01T00:00:00Z","file":[{"creator":"larathoo","file_id":"11412","access_level":"open_access","success":1,"relation":"main_file","file_name":"Manuscript.pdf","content_type":"application/pdf","date_updated":"2022-05-26T12:48:15Z","file_size":885374,"checksum":"cc2d56deb608bd53c5cc02f03a875107","date_created":"2022-05-26T12:48:15Z"},{"date_created":"2022-05-26T12:48:21Z","file_size":1401704,"checksum":"693742595b6c7ed809423be01460d083","date_updated":"2022-05-26T12:48:21Z","content_type":"application/pdf","file_name":"SupplementalMaterial.pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"11413","creator":"larathoo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14651"},{"status":"public","relation":"research_data","id":"11321"},{"relation":"research_data","id":"9192","status":"public"}]}},{"acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","volume":120,"date_updated":"2023-08-03T07:16:20Z","year":"2022","citation":{"mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>.","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401.","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>","ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022.","chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>."},"isi":1,"external_id":{"isi":["000796002100002"]},"doi":"10.1063/5.0097339","day":"12","abstract":[{"text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n","lang":"eng"}],"quality_controlled":"1","publisher":"American Institute of Physics","article_type":"letter_note","_id":"11417","scopus_import":"1","author":[{"first_name":"Anthony J.","last_name":"Sigillito","full_name":"Sigillito, Anthony J."},{"first_name":"Jacob P.","last_name":"Covey","full_name":"Covey, Jacob P."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"full_name":"Petersson, Karl","last_name":"Petersson","first_name":"Karl"},{"full_name":"Preble, Stefan","first_name":"Stefan","last_name":"Preble"}],"issue":"19","publication_status":"published","date_created":"2022-05-29T22:01:53Z","department":[{"_id":"JoFi"}],"article_processing_charge":"No","title":"Emerging qubit systems: Guest editorial","intvolume":"       120","main_file_link":[{"url":"https://doi.org/10.1063/5.0097339","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-05-12T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0003-6951"]},"oa":1,"language":[{"iso":"eng"}],"publication":"Applied Physics Letters","oa_version":"Published Version","month":"05","article_number":"190401"},{"quality_controlled":"1","page":"984-1012","article_type":"original","publisher":"Institute of Mathematical Statistics","issue":"3","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio"},{"first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"11418","intvolume":"        50","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","department":[{"_id":"LaEr"}],"date_created":"2022-05-29T22:01:53Z","article_processing_charge":"No","publication_status":"published","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","volume":50,"external_id":{"arxiv":["2103.06730"],"isi":["000793963400005"]},"isi":1,"year":"2022","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>."},"date_updated":"2023-08-03T07:16:53Z","abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"day":"01","arxiv":1,"doi":"10.1214/21-AOP1552","language":[{"iso":"eng"}],"publication":"Annals of Probability","month":"05","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"type":"journal_article","date_published":"2022-05-01T00:00:00Z","oa":1,"publication_identifier":{"eissn":["2168-894X"],"issn":["0091-1798"]}},{"volume":11,"acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","ddc":["616"],"day":"05","doi":"10.7554/eLife.73542","abstract":[{"text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission.","lang":"eng"}],"citation":{"ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>.","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542."},"year":"2022","date_updated":"2023-08-03T07:15:49Z","external_id":{"isi":["000876231600001"],"pmid":["35471147 "]},"isi":1,"publisher":"eLife Sciences Publications","article_type":"original","quality_controlled":"1","file_date_updated":"2022-05-30T08:09:16Z","department":[{"_id":"RySh"}],"article_processing_charge":"No","date_created":"2022-05-29T22:01:54Z","publication_status":"published","intvolume":"        11","title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","scopus_import":"1","pmid":1,"_id":"11419","author":[{"full_name":"Hori, Tetsuya","last_name":"Hori","first_name":"Tetsuya"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546"},{"last_name":"Wang","first_name":"Han Ying","full_name":"Wang, Han Ying"},{"full_name":"Miyasaka, Tomohiro","first_name":"Tomohiro","last_name":"Miyasaka"},{"full_name":"Guillaud, Laurent","first_name":"Laurent","last_name":"Guillaud"},{"first_name":"Zacharie","last_name":"Taoufiq","full_name":"Taoufiq, Zacharie"},{"last_name":"Mahapatra","first_name":"Satyajit","full_name":"Mahapatra, Satyajit"},{"first_name":"Hiroshi","last_name":"Yamada","full_name":"Yamada, Hiroshi"},{"full_name":"Takei, Kohji","last_name":"Takei","first_name":"Kohji"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"file":[{"access_level":"open_access","success":1,"relation":"main_file","file_id":"11421","creator":"cchlebak","date_created":"2022-05-30T08:09:16Z","file_size":2466296,"checksum":"ccddbd167e00ff8375f12998af497152","date_updated":"2022-05-30T08:09:16Z","content_type":"application/pdf","file_name":"elife-73542-v2.pdf"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-05-05T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"e73542","month":"05","has_accepted_license":"1","publication":"eLife"},{"ddc":["000"],"volume":23,"acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","external_id":{"arxiv":["2111.02278"]},"citation":{"ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","chicago":"Shevchenko, Aleksandr, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","mla":"Shevchenko, Aleksandr, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55."},"year":"2022","date_updated":"2024-09-10T13:03:17Z","abstract":[{"lang":"eng","text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory."}],"day":"01","arxiv":1,"file_date_updated":"2022-05-30T08:22:55Z","quality_controlled":"1","page":"1-55","article_type":"original","publisher":"Journal of Machine Learning Research","issue":"130","author":[{"last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Kungurtsev, Vyacheslav","last_name":"Kungurtsev","first_name":"Vyacheslav"},{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"scopus_import":"1","_id":"11420","intvolume":"        23","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","date_created":"2022-05-29T22:01:54Z","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"article_processing_charge":"No","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","related_material":{"link":[{"url":"https://www.jmlr.org/papers/v23/21-1365.html","relation":"other"}]},"file":[{"access_level":"open_access","success":1,"relation":"main_file","creator":"cchlebak","file_id":"11422","file_size":1521701,"checksum":"d4ff5d1affb34848b5c5e4002483fc62","date_created":"2022-05-30T08:22:55Z","file_name":"21-1365.pdf","content_type":"application/pdf","date_updated":"2022-05-30T08:22:55Z"}],"type":"journal_article","date_published":"2022-04-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Journal of Machine Learning Research","month":"04","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa_version":"Published Version"},{"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2022-06-07","location":"Berlin, Germany","end_date":"2022-06-10"},"language":[{"iso":"eng"}],"project":[{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"},{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa_version":"Published Version","month":"06","has_accepted_license":"1","publication":"38th International Symposium on Computational Geometry","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"11437","creator":"dernst","date_created":"2022-06-07T07:58:30Z","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","file_size":17580705,"date_updated":"2022-06-07T07:58:30Z","content_type":"application/pdf","file_name":"2022_LIPICs_Chambers.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"isbn":["978-3-95977-227-3"],"issn":["1868-8969"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","date_published":"2022-06-01T00:00:00Z","editor":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","series_title":"LIPIcs","ec_funded":1,"page":"66:1-66:9","file_date_updated":"2022-06-07T07:58:30Z","article_processing_charge":"No","date_created":"2022-06-01T14:18:04Z","department":[{"_id":"HeEd"}],"publication_status":"published","intvolume":"       224","title":"A cautionary tale: Burning the medial axis is unstable","scopus_import":"1","_id":"11428","author":[{"last_name":"Chambers","first_name":"Erin","full_name":"Chambers, Erin"},{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D","first_name":"Christopher D","last_name":"Fillmore"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R","last_name":"Stephenson","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"Partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics” and the European Research Council (ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing code to generate the examples.","volume":224,"ddc":["510"],"day":"01","doi":"10.4230/LIPIcs.SoCG.2022.66","abstract":[{"lang":"eng","text":"The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible."}],"year":"2022","citation":{"ista":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary tale: Burning the medial axis is unstable. 38th International Symposium on Computational Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.","mla":"Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>.","short":"E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc, M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.","ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.","chicago":"Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>.","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>","ama":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale: Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. <i>38th International Symposium on Computational Geometry</i>. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022:66:1-66:9. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>"},"date_updated":"2023-02-21T09:50:52Z"},{"language":[{"iso":"eng"}],"quality_controlled":"1","page":"153","editor":[{"last_name":"Karimipour","first_name":"Farid","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"},{"full_name":"Storandt, Sabine","last_name":"Storandt","first_name":"Sabine"}],"publisher":"Springer Nature","_id":"11429","intvolume":"     13238","month":"05","alternative_title":["LNCS"],"title":"Web and Wireless Geographical Information Systems","date_created":"2022-06-02T05:40:53Z","article_processing_charge":"No","department":[{"_id":"HeEd"}],"oa_version":"None","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","volume":13238,"type":"book_editor","date_published":"2022-05-01T00:00:00Z","year":"2022","citation":{"chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p.","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>.","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022."},"date_updated":"2022-06-02T05:56:22Z","abstract":[{"text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.","lang":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783031062452"],"isbn":["9783031062445"]},"day":"01","edition":"1","doi":"10.1007/978-3-031-06245-2"},{"volume":41,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","abstract":[{"text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics.","lang":"eng"}],"day":"01","doi":"10.1111/cgf.14478","external_id":{"isi":["000802723900027"]},"isi":1,"citation":{"ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.","mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>"},"year":"2022","date_updated":"2023-08-02T06:44:05Z","article_type":"original","publisher":"Wiley","ec_funded":1,"quality_controlled":"1","page":"343-353","intvolume":"        41","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","department":[{"_id":"ChWo"}],"article_processing_charge":"No","date_created":"2022-06-05T22:01:49Z","publication_status":"published","issue":"2","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille","full_name":"Schreck, Camille"},{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"11432","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"type":"journal_article","date_published":"2022-05-01T00:00:00Z","language":[{"iso":"eng"}],"month":"05","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"Computer Graphics Forum"},{"publisher":"Society for Industrial and Applied Mathematics","article_type":"original","quality_controlled":"1","page":"951-957","article_processing_charge":"No","department":[{"_id":"UlWa"}],"date_created":"2022-06-05T22:01:50Z","publication_status":"published","intvolume":"        36","title":"A quantitative Helly-type theorem: Containment in a homothet","scopus_import":"1","_id":"11435","issue":"2","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"full_name":"Naszodi, Marton","last_name":"Naszodi","first_name":"Marton"}],"volume":36,"acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","day":"11","arxiv":1,"doi":"10.1137/21M1403308","abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"year":"2022","citation":{"chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022.","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>","ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957."},"date_updated":"2023-10-18T06:58:03Z","external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"isi":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","month":"04","publication":"SIAM Journal on Discrete Mathematics","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.04122","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["0895-4801"]},"oa":1,"type":"journal_article","date_published":"2022-04-11T00:00:00Z"},{"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy"],"oa_version":"Preprint","month":"05","article_number":"054031","publication":"Physical Review Applied","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.13194"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["2331-7019"]},"oa":1,"date_published":"2022-05-19T00:00:00Z","type":"journal_article","publisher":"American Physical Society","article_type":"original","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_created":"2022-06-07T08:07:59Z","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"title":"Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters","intvolume":"        17","_id":"11438","author":[{"full_name":"Li, Vyacheslav","first_name":"Vyacheslav","last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Diorico, Fritz R","first_name":"Fritz R","last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur"}],"issue":"5","acknowledgement":"This work was supported by IST Austria. The authors thank Yueheng Shi for technical contributions.","volume":17,"arxiv":1,"doi":"10.1103/physrevapplied.17.054031","day":"19","abstract":[{"lang":"eng","text":"Lasers with well-controlled relative frequencies are indispensable for many applications in science and technology. We present a frequency-offset locking method for lasers based on beat-frequency discrimination utilizing hybrid electronic LC filters. The method is specifically designed for decoupling the tightness of the lock from the broadness of its capture range. The presented demonstration locks two free-running diode lasers at 780 nm with a 5.5-GHz offset. It displays an offset frequency instability below 55 Hz for time scales in excess of 1000 s and a minimum of 12 Hz at 10-s averaging. The performance is complemented with a 190-MHz lock-capture range, a tuning range of up to 1 GHz, and a frequency ramp agility of 200kHz/μs."}],"date_updated":"2023-08-03T07:18:34Z","year":"2022","citation":{"ieee":"V. Li, F. R. Diorico, and O. Hosten, “Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters,” <i>Physical Review Applied</i>, vol. 17, no. 5. American Physical Society, 2022.","chicago":"Li, Vyacheslav, Fritz R Diorico, and Onur Hosten. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>.","apa":"Li, V., Diorico, F. R., &#38; Hosten, O. (2022). Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>","ama":"Li V, Diorico FR, Hosten O. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. 2022;17(5). doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>","ista":"Li V, Diorico FR, Hosten O. 2022. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. Physical Review Applied. 17(5), 054031.","short":"V. Li, F.R. Diorico, O. Hosten, Physical Review Applied 17 (2022).","mla":"Li, Vyacheslav, et al. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>, vol. 17, no. 5, 054031, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>."},"isi":1,"external_id":{"isi":["000880670300001"],"arxiv":["2111.13194"]}},{"publication":"Research in Computational Topology 2","oa_version":"Preprint","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"month":"01","language":[{"iso":"eng"}],"date_published":"2022-01-27T00:00:00Z","type":"book_chapter","publication_identifier":{"eisbn":["9783030955199"],"isbn":["9783030955182"]},"oa":1,"place":"Cham","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2102.11397"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11440","scopus_import":"1","author":[{"full_name":"Bleile, Bea","first_name":"Bea","last_name":"Bleile"},{"full_name":"Garin, Adélie","first_name":"Adélie","last_name":"Garin"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","first_name":"Teresa","full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689"},{"full_name":"Maggs, Kelly","first_name":"Kelly","last_name":"Maggs"},{"full_name":"Robins, Vanessa","last_name":"Robins","first_name":"Vanessa"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"HeEd"}],"date_created":"2022-06-07T08:21:11Z","alternative_title":["Association for Women in Mathematics Series"],"title":"The persistent homology of dual digital image constructions","intvolume":"        30","page":"1-26","quality_controlled":"1","ec_funded":1,"series_title":"AWMS","publisher":"Springer Nature","editor":[{"full_name":"Gasparovic, Ellen","first_name":"Ellen","last_name":"Gasparovic"},{"last_name":"Robins","first_name":"Vanessa","full_name":"Robins, Vanessa"},{"full_name":"Turner, Katharine","last_name":"Turner","first_name":"Katharine"}],"date_updated":"2022-06-07T08:32:42Z","year":"2022","citation":{"ieee":"B. Bleile, A. Garin, T. Heiss, K. Maggs, and V. Robins, “The persistent homology of dual digital image constructions,” in <i>Research in Computational Topology 2</i>, 1st ed., vol. 30, E. Gasparovic, V. Robins, and K. Turner, Eds. Cham: Springer Nature, 2022, pp. 1–26.","chicago":"Bleile, Bea, Adélie Garin, Teresa Heiss, Kelly Maggs, and Vanessa Robins. “The Persistent Homology of Dual Digital Image Constructions.” In <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic, Vanessa Robins, and Katharine Turner, 1st ed., 30:1–26. AWMS. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>.","apa":"Bleile, B., Garin, A., Heiss, T., Maggs, K., &#38; Robins, V. (2022). The persistent homology of dual digital image constructions. In E. Gasparovic, V. Robins, &#38; K. Turner (Eds.), <i>Research in Computational Topology 2</i> (1st ed., Vol. 30, pp. 1–26). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>","ama":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. The persistent homology of dual digital image constructions. In: Gasparovic E, Robins V, Turner K, eds. <i>Research in Computational Topology 2</i>. Vol 30. 1st ed. AWMS. Cham: Springer Nature; 2022:1-26. doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>","ista":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. 2022.The persistent homology of dual digital image constructions. In: Research in Computational Topology 2. Association for Women in Mathematics Series, vol. 30, 1–26.","short":"B. Bleile, A. Garin, T. Heiss, K. Maggs, V. Robins, in:, E. Gasparovic, V. Robins, K. Turner (Eds.), Research in Computational Topology 2, 1st ed., Springer Nature, Cham, 2022, pp. 1–26.","mla":"Bleile, Bea, et al. “The Persistent Homology of Dual Digital Image Constructions.” <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic et al., 1st ed., vol. 30, Springer Nature, 2022, pp. 1–26, doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>."},"external_id":{"arxiv":["2102.11397"]},"doi":"10.1007/978-3-030-95519-9_1","arxiv":1,"edition":"1","day":"27","abstract":[{"text":"To compute the persistent homology of a grayscale digital image one needs to build a simplicial or cubical complex from it. For cubical complexes, the two commonly used constructions (corresponding to direct and indirect digital adjacencies) can give different results for the same image. The two constructions are almost dual to each other, and we use this relationship to extend and modify the cubical complexes to become dual filtered cell complexes. We derive a general relationship between the persistent homology of two dual filtered cell complexes, and also establish how various modifications to a filtered complex change the persistence diagram. Applying these results to images, we derive a method to transform the persistence diagram computed using one type of cubical complex into a persistence diagram for the other construction. This means software for computing persistent homology from images can now be easily adapted to produce results for either of the two cubical complex constructions without additional low-level code implementation.","lang":"eng"}],"volume":30,"acknowledgement":"This project started during the Women in Computational Topology workshop held in Canberra in July of 2019. All authors are very grateful for its organisation and the financial support for the workshop from the Mathematical Sciences Institute at ANU, the US National Science Foundation through the award CCF-1841455, the Australian Mathematical Sciences Institute and the Association for Women in Mathematics. AG is supported by the Swiss National Science Foundation grant CRSII5_177237. TH is supported by the European Research Council (ERC) Horizon 2020 project “Alpha Shape Theory Extended” No. 788183. KM is supported by the ERC Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 859860. VR was supported by Australian Research Council Future Fellowship FT140100604 during the early stages of this project."},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-06-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"oa":1,"file":[{"file_size":33994829,"checksum":"27f6fe41c6ff84d50445cc9b0176d45b","date_created":"2022-06-28T08:32:58Z","content_type":"application/pdf","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","date_updated":"2022-06-28T08:32:58Z","access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","file_id":"11467"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/"}]},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","oa_version":"Submitted Version","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"month":"06","article_number":"112","language":[{"iso":"eng"}],"date_updated":"2023-05-31T12:38:21Z","year":"2022","citation":{"ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>"},"external_id":{"arxiv":["2201.11819"]},"arxiv":1,"doi":"10.1145/3528223.3530144","day":"01","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"volume":41,"acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","ddc":["000"],"_id":"11442","author":[{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"full_name":"Foshey, Michael","last_name":"Foshey","first_name":"Michael"},{"full_name":"Xu, Jie","first_name":"Jie","last_name":"Xu"},{"last_name":"Erps","first_name":"Timothy","full_name":"Erps, Timothy"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Rusinkiewicz, Szymon","first_name":"Szymon","last_name":"Rusinkiewicz"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","publication_status":"published","article_processing_charge":"No","department":[{"_id":"BeBi"}],"date_created":"2022-06-10T06:41:47Z","title":"Closed-loop control of direct ink writing via reinforcement learning","intvolume":"        41","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-06-28T08:32:58Z","publisher":"Association for Computing Machinery","article_type":"original"}]