[{"date_created":"2021-02-23T12:31:43Z","year":"2021","isi":1,"_id":"9188","intvolume":"       145","language":[{"iso":"eng"}],"keyword":["Cell Biology","Cellular and Molecular Neuroscience"],"day":"01","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"file":[{"file_name":"2021_NCI_Pauler.pdf","file_id":"9883","creator":"kschuh","success":1,"date_updated":"2021-08-11T12:30:38Z","date_created":"2021-08-11T12:30:38Z","file_size":7083499,"relation":"main_file","content_type":"application/pdf","checksum":"c6d7a40089cd29e289f9b22e75768304","access_level":"open_access"}],"ec_funded":1,"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"5","publication_identifier":{"issn":["0197-0186"]},"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues."}],"type":"journal_article","department":[{"_id":"SiHi"}],"ddc":["570"],"article_type":"original","external_id":{"pmid":["33600873"],"isi":["000635575000005"]},"article_number":"104986","title":"Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond","date_published":"2021-05-01T00:00:00Z","status":"public","pmid":1,"doi":"10.1016/j.neuint.2021.104986","oa_version":"Published Version","citation":{"ama":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. 2021;145(5). doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>","apa":"Pauler, F., Hudson, Q., Laukoter, S., &#38; Hippenmeyer, S. (2021). Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>","ista":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. 145(5), 104986.","ieee":"F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond,” <i>Neurochemistry International</i>, vol. 145, no. 5. Elsevier, 2021.","chicago":"Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>.","mla":"Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>, vol. 145, no. 5, 104986, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>.","short":"F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International 145 (2021)."},"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"last_name":"Hudson","first_name":"Quanah","full_name":"Hudson, Quanah"},{"first_name":"Susanne","full_name":"Laukoter, Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file_date_updated":"2021-08-11T12:30:38Z","publication_status":"published","has_accepted_license":"1","acknowledgement":"We thank Melissa Stouffer for critically reading the manuscript. This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung n[f + b] life science call grant (C13-002) to S.H. and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","month":"05","quality_controlled":"1","publication":"Neurochemistry International","date_updated":"2025-04-14T07:43:04Z","volume":145},{"page":"1846-1857","article_type":"original","type":"journal_article","abstract":[{"lang":"eng","text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses."}],"ddc":["580"],"department":[{"_id":"JiFr"}],"pmid":1,"doi":"10.1111/pce.14029","oa_version":"Submitted Version","citation":{"ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. 2021;44(6):1846-1857. doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>","ieee":"Y. Zhao <i>et al.</i>, “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. Wiley. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell &#38; Environment. 44(6), 1846–1857.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell &#38; Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>."},"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Zhao","first_name":"Y","full_name":"Zhao, Y"},{"last_name":"Wu","full_name":"Wu, L","first_name":"L"},{"first_name":"Q","full_name":"Fu, Q","last_name":"Fu"},{"last_name":"Wang","full_name":"Wang, D","first_name":"D"},{"first_name":"J","full_name":"Li, J","last_name":"Li"},{"last_name":"Yao","first_name":"B","full_name":"Yao, B"},{"last_name":"Yu","full_name":"Yu, S","first_name":"S"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"last_name":"Qian","first_name":"J","full_name":"Qian, J"},{"full_name":"Zhou, X","first_name":"X","last_name":"Zhou"},{"last_name":"Han","full_name":"Han, L","first_name":"L"},{"full_name":"Zhao, S","first_name":"S","last_name":"Zhao"},{"last_name":"Ma","first_name":"C","full_name":"Ma, C"},{"last_name":"Zhang","full_name":"Zhang, Y","first_name":"Y"},{"first_name":"C","full_name":"Luo, C","last_name":"Luo"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"first_name":"S","full_name":"Li, S","last_name":"Li"},{"last_name":"Zhang","full_name":"Zhang, L","first_name":"L"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Luo","first_name":"H","full_name":"Luo, H"},{"last_name":"Li","first_name":"K","full_name":"Li, K"},{"full_name":"Yang, J","first_name":"J","last_name":"Yang"},{"first_name":"Q","full_name":"Luo, Q","last_name":"Luo"},{"last_name":"Li","first_name":"L","full_name":"Li, L"},{"last_name":"Peng","full_name":"Peng, S","first_name":"S"},{"last_name":"Huang","full_name":"Huang, H","first_name":"H"},{"full_name":"Zuo, Z","first_name":"Z","last_name":"Zuo"},{"first_name":"C","full_name":"Liu, C","last_name":"Liu"},{"first_name":"L","full_name":"Wang, L","last_name":"Wang"},{"first_name":"C","full_name":"Li, C","last_name":"Li"},{"full_name":"He, X","first_name":"X","last_name":"He"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Du","full_name":"Du, Y","first_name":"Y"}],"external_id":{"isi":["000625398600001"],"pmid":["33576018"]},"date_published":"2021-06-01T00:00:00Z","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","status":"public","has_accepted_license":"1","oa":1,"file_date_updated":"2023-11-02T17:02:11Z","publication_status":"published","date_updated":"2023-11-07T08:18:36Z","volume":44,"quality_controlled":"1","month":"06","publication":"Plant, Cell & Environment","isi":1,"date_created":"2021-02-24T10:07:21Z","year":"2021","_id":"9189","intvolume":"        44","language":[{"iso":"eng"}],"day":"01","file":[{"relation":"main_file","file_size":8437528,"date_created":"2023-11-02T17:02:11Z","access_level":"open_access","content_type":"application/pdf","checksum":"a812418fede076741c9c4dc07f317068","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","date_updated":"2023-11-02T17:02:11Z","creator":"amally","file_id":"14481","success":1}],"scopus_import":"1","issue":"6","publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document."}],"type":"research_data","date_created":"2021-02-24T17:49:21Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"ddc":["576"],"year":"2021","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","date_published":"2021-02-26T00:00:00Z","status":"public","doi":"10.15479/AT:ISTA:9192","_id":"9192","oa_version":"Published Version","day":"26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8254"},{"id":"11321","status":"public","relation":"later_version"},{"id":"11411","relation":"used_in_publication","status":"public"}]},"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>.","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","orcid":"0000-0001-6395-386X"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","full_name":"Arathoon, Louise S","first_name":"Louise S"},{"orcid":"0000-0002-7354-8574","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","full_name":"Baskett, Carina"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"full_name":"Pickup, Melinda","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"file":[{"creator":"larathoo","file_id":"9193","success":1,"date_updated":"2021-02-24T17:45:13Z","file_name":"Data_Code.zip","checksum":"f85537815809a8a4b7da9d01163f88c0","content_type":"application/x-zip-compressed","access_level":"open_access","file_size":5934452,"date_created":"2021-02-24T17:45:13Z","relation":"main_file"}],"oa":1,"file_date_updated":"2021-02-24T17:45:13Z","has_accepted_license":"1","month":"02","date_updated":"2025-04-15T08:20:40Z","article_processing_charge":"No","contributor":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member"},{"orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"David"},{"first_name":"Melinda","contributor_type":"project_member","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","contributor_type":"project_leader","first_name":"Nicholas H"}]},{"date_created":"2021-02-26T16:30:39Z","year":"2021","conference":{"end_date":"2021-05-21","location":"Nashville, TN, United States","start_date":"2021-05-19","name":"HSCC: Hybrid Systems - Computation and Control"},"isi":1,"corr_author":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2021-05-25T13:53:22Z","creator":"kschuh","success":1,"file_id":"9424","file_name":"2021_HSCC_Soto.pdf","content_type":"application/pdf","checksum":"4c1202c1abf71384c3ee6fea88c2f80e","access_level":"open_access","relation":"main_file","file_size":1474786,"date_created":"2021-05-25T13:53:22Z"}],"_id":"9200","language":[{"iso":"eng"}],"keyword":["hybrid automaton","membership","system identification"],"day":"01","ec_funded":1,"publication_identifier":{"isbn":["9781450383394"]},"scopus_import":"1","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"article_processing_charge":"No","type":"conference","abstract":[{"lang":"eng","text":"Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach."}],"department":[{"_id":"ToHe"}],"ddc":["000"],"page":"2102.12734","status":"public","external_id":{"isi":["000932821700028"],"arxiv":["2102.12734"]},"date_published":"2021-05-01T00:00:00Z","title":"Synthesis of hybrid automata with affine dynamics from time-series data","publisher":"Association for Computing Machinery","citation":{"chicago":"Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, 2102.12734. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734.","mla":"Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Association for Computing Machinery, 2021, p. 2102.12734, doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>.","ama":"Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with affine dynamics from time-series data. In: <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>. Association for Computing Machinery; 2021:2102.12734. doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>","ieee":"M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata with affine dynamics from time-series data,” in <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Nashville, TN, United States, 2021, p. 2102.12734.","apa":"Garcia Soto, M., Henzinger, T. A., &#38; Schilling, C. (2021). Synthesis of hybrid automata with affine dynamics from time-series data. In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i> (p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>","ista":"Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 2102.12734."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Garcia Soto, Miriam","first_name":"Miriam","orcid":"0000-0003-2936-5719","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling"}],"doi":"10.1145/3447928.3456704","oa_version":"Published Version","publication_status":"published","oa":1,"file_date_updated":"2021-05-25T13:53:22Z","has_accepted_license":"1","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","publication":"HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control","arxiv":1,"quality_controlled":"1","month":"05","date_updated":"2025-07-10T12:01:40Z"},{"article_processing_charge":"No","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_identifier":{"eissn":["2589-0042"]},"issue":"3","scopus_import":"1","ec_funded":1,"file":[{"creator":"dernst","file_id":"9219","success":1,"date_updated":"2021-03-03T07:38:14Z","file_name":"2021_iScience_Kampjut.pdf","access_level":"open_access","checksum":"50585447386fe5842f07ab9b3a66e7e9","content_type":"application/pdf","file_size":7431411,"date_created":"2021-03-03T07:38:14Z","relation":"main_file"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"day":"19","_id":"9205","intvolume":"        24","language":[{"iso":"eng"}],"isi":1,"year":"2021","date_created":"2021-02-28T23:01:24Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"volume":24,"date_updated":"2026-04-02T14:00:19Z","publication":"iScience","month":"03","quality_controlled":"1","acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","has_accepted_license":"1","publication_status":"published","file_date_updated":"2021-03-03T07:38:14Z","oa":1,"author":[{"full_name":"Kampjut, Domen","first_name":"Domen","orcid":"0000-0002-6018-3422","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut"},{"first_name":"Julia","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"publisher":"Elsevier","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>.","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>, vol. 24, no. 3, 102139, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).","ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139.","apa":"Kampjut, D., Steiner, J., &#38; Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021."},"oa_version":"Published Version","pmid":1,"doi":"10.1016/j.isci.2021.102139","status":"public","article_number":"102139","title":"Cryo-EM grid optimization for membrane proteins","date_published":"2021-03-19T00:00:00Z","external_id":{"isi":["000631646000012"],"pmid":["33665558"]},"article_type":"original","ddc":["570"],"department":[{"_id":"LeSa"}],"type":"journal_article","abstract":[{"text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.","lang":"eng"}]},{"publication_identifier":{"eissn":["1996-1944"]},"scopus_import":"1","issue":"4","article_processing_charge":"No","year":"2021","date_created":"2021-02-28T23:01:24Z","isi":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2021_Materials_Cadavid.pdf","success":1,"creator":"dernst","file_id":"9218","date_updated":"2021-03-03T07:32:01Z","file_size":2722517,"date_created":"2021-03-03T07:32:01Z","relation":"main_file","access_level":"open_access","checksum":"76d6c7f97b810ce504ab151c9bf3524e","content_type":"application/pdf"}],"intvolume":"        14","_id":"9206","language":[{"iso":"eng"}],"day":"10","publication_status":"published","oa":1,"file_date_updated":"2021-03-03T07:32:01Z","acknowledgement":"This work was supported by European Regional Development Funds and the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges support from the US National Science Foundation under grant No. DMR-1748188. DC acknowledges support from COLCIENCIAS under project 120480863414. ","has_accepted_license":"1","publication":"Materials","month":"02","quality_controlled":"1","volume":14,"date_updated":"2025-06-12T06:35:03Z","type":"journal_article","abstract":[{"lang":"eng","text":"The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. "}],"department":[{"_id":"MaIb"}],"ddc":["540"],"article_type":"original","status":"public","external_id":{"isi":["000624094100001"],"pmid":["33578981"]},"date_published":"2021-02-10T00:00:00Z","title":"Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks","article_number":"853","publisher":"MDPI","citation":{"chicago":"Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>.","short":"D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez, A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021).","mla":"Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>, vol. 14, no. 4, 853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>.","ama":"Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. 2021;14(4). doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>","ieee":"D. Cadavid <i>et al.</i>, “Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks,” <i>Materials</i>, vol. 14, no. 4. MDPI, 2021.","ista":"Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853.","apa":"Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021). Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"last_name":"Wei","full_name":"Wei, Kaya","first_name":"Kaya"},{"full_name":"Liu, Yu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"first_name":"Taisiia","full_name":"Berestok, Taisiia","last_name":"Berestok"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"full_name":"Nolas, George S.","first_name":"George S.","last_name":"Nolas"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"doi":"10.3390/ma14040853","pmid":1,"oa_version":"Published Version"},{"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"b8020d6338667673e34fde0608913dd2","file_size":4124471,"date_created":"2021-03-03T09:49:34Z","relation":"main_file","creator":"dernst","success":1,"file_id":"9220","date_updated":"2021-03-03T09:49:34Z","file_name":"2021_JourFluidMechanics_Klotz.pdf"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"15","_id":"9207","intvolume":"       912","language":[{"iso":"eng"}],"isi":1,"date_created":"2021-02-28T23:01:25Z","year":"2021","article_processing_charge":"Yes (via OA deal)","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"scopus_import":"1","ec_funded":1,"author":[{"full_name":"Klotz, Lukasz","first_name":"Lukasz","orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","last_name":"Klotz"},{"full_name":"Pavlenko, A. M.","first_name":"A. M.","last_name":"Pavlenko"},{"first_name":"J. E.","full_name":"Wesfreid, J. E.","last_name":"Wesfreid"}],"publisher":"Cambridge University Press","citation":{"short":"L. Klotz, A.M. Pavlenko, J.E. Wesfreid, Journal of Fluid Mechanics 912 (2021).","mla":"Klotz, Lukasz, et al. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>, vol. 912, A24, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>.","chicago":"Klotz, Lukasz, A. M. Pavlenko, and J. E. Wesfreid. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>.","ista":"Klotz L, Pavlenko AM, Wesfreid JE. 2021. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. 912, A24.","apa":"Klotz, L., Pavlenko, A. M., &#38; Wesfreid, J. E. (2021). Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>","ieee":"L. Klotz, A. M. Pavlenko, and J. E. Wesfreid, “Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow,” <i>Journal of Fluid Mechanics</i>, vol. 912. Cambridge University Press, 2021.","ama":"Klotz L, Pavlenko AM, Wesfreid JE. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. 2021;912. doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","doi":"10.1017/jfm.2020.1089","status":"public","title":"Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow","article_number":"A24","date_published":"2021-02-15T00:00:00Z","external_id":{"isi":["000618034400001"]},"article_type":"original","department":[{"_id":"BjHo"}],"ddc":["530"],"abstract":[{"lang":"eng","text":"In this paper we experimentally study the transitional range of Reynolds numbers in\r\nplane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures\r\ntriggered by a strong impulsive jet and the large-scale flow generated around these\r\nstructures. We present a detailed investigation of the large-scale flow and show how\r\nits amplitude depends on Reynolds number and amplitude perturbation. In addition,\r\nwe characterize the initial dynamics of the localized turbulent spot, which includes the\r\ncoupling between the small and large scales, as well as the dependence of the advection\r\nspeed on the large-scale flow generated around the spot. Finally, we provide the first\r\nexperimental measurements of the large-scale flow around an oblique turbulent band."}],"type":"journal_article","volume":912,"date_updated":"2025-04-14T07:43:51Z","publication":"Journal of Fluid Mechanics","month":"02","quality_controlled":"1","has_accepted_license":"1","acknowledgement":"We thank Y. Duguet, S. Gomé, G. Lemoult, T. Liu, B. Semin and L.S. Tuckerman for\r\nfruitful discussions. \r\nThis work was supported by a grant, TRANSFLOW, provided by the Agence Nationale de\r\nla Recherche (ANR). A.M.P. was partially supported by the French Embassy in Russia (I.I. Mechnikov scholarship) and by the Russian Science Foundation (project no. 18-79-00189). L.K. was partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","publication_status":"published","file_date_updated":"2021-03-03T09:49:34Z","oa":1},{"isi":1,"conference":{"start_date":"2020-09-28","name":"DAGM GCPR: German Conference on Pattern Recognition ","location":"Tübingen, Germany","end_date":"2020-10-01"},"date_created":"2021-03-01T09:01:16Z","year":"2021","day":"17","intvolume":"     12544","_id":"9210","language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":420234,"date_created":"2022-08-12T07:27:58Z","access_level":"open_access","content_type":"application/pdf","checksum":"3e3628ab1cf658d82524963f808004ea","file_name":"2020_GCPR_submitted_Volhejn.pdf","date_updated":"2022-08-12T07:27:58Z","success":1,"file_id":"11820","creator":"dernst"}],"scopus_import":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030712778"],"issn":["0302-9743"]},"article_processing_charge":"No","page":"246-259","ddc":["510"],"series_title":"LNCS","department":[{"_id":"ChLa"}],"abstract":[{"text":"Modern neural networks can easily fit their training set perfectly. Surprisingly, despite being “overfit” in this way, they tend to generalize well to future data, thereby defying the classic bias–variance trade-off of machine learning theory. Of the many possible explanations, a prevalent one is that training by stochastic gradient descent (SGD) imposes an implicit bias that leads it to learn simple functions, and these simple functions generalize well. However, the specifics of this implicit bias are not well understood.\r\nIn this work, we explore the smoothness conjecture which states that SGD is implicitly biased towards learning functions that are smooth. We propose several measures to formalize the intuitive notion of smoothness, and we conduct experiments to determine whether SGD indeed implicitly optimizes for these measures. Our findings rule out the possibility that smoothness measures based on first-order derivatives are being implicitly enforced. They are supportive, though, of the smoothness conjecture for measures based on second-order derivatives.","lang":"eng"}],"type":"conference","oa_version":"Submitted Version","doi":"10.1007/978-3-030-71278-5_18","author":[{"full_name":"Volhejn, Vaclav","first_name":"Vaclav","last_name":"Volhejn","id":"d5235fb4-7a6d-11eb-b254-f25d12d631a8"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","citation":{"chicago":"Volhejn, Vaclav, and Christoph Lampert. “Does SGD Implicitly Optimize for Smoothness?” In <i>42nd German Conference on Pattern Recognition</i>, 12544:246–59. LNCS. Springer, 2021. <a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">https://doi.org/10.1007/978-3-030-71278-5_18</a>.","mla":"Volhejn, Vaclav, and Christoph Lampert. “Does SGD Implicitly Optimize for Smoothness?” <i>42nd German Conference on Pattern Recognition</i>, vol. 12544, Springer, 2021, pp. 246–59, doi:<a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">10.1007/978-3-030-71278-5_18</a>.","short":"V. Volhejn, C. Lampert, in:, 42nd German Conference on Pattern Recognition, Springer, 2021, pp. 246–259.","ama":"Volhejn V, Lampert C. Does SGD implicitly optimize for smoothness? In: <i>42nd German Conference on Pattern Recognition</i>. Vol 12544. LNCS. Springer; 2021:246-259. doi:<a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">10.1007/978-3-030-71278-5_18</a>","apa":"Volhejn, V., &#38; Lampert, C. (2021). Does SGD implicitly optimize for smoothness? In <i>42nd German Conference on Pattern Recognition</i> (Vol. 12544, pp. 246–259). Tübingen, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-71278-5_18\">https://doi.org/10.1007/978-3-030-71278-5_18</a>","ista":"Volhejn V, Lampert C. 2021. Does SGD implicitly optimize for smoothness? 42nd German Conference on Pattern Recognition. DAGM GCPR: German Conference on Pattern Recognition LNCS vol. 12544, 246–259.","ieee":"V. Volhejn and C. Lampert, “Does SGD implicitly optimize for smoothness?,” in <i>42nd German Conference on Pattern Recognition</i>, Tübingen, Germany, 2021, vol. 12544, pp. 246–259."},"date_published":"2021-03-17T00:00:00Z","title":"Does SGD implicitly optimize for smoothness?","external_id":{"isi":["001500603200018"]},"status":"public","has_accepted_license":"1","file_date_updated":"2022-08-12T07:27:58Z","oa":1,"publication_status":"published","date_updated":"2025-09-10T10:00:33Z","volume":12544,"quality_controlled":"1","month":"03","publication":"42nd German Conference on Pattern Recognition"},{"publication":"Cold Spring Harbor Perspectives in Biology","quality_controlled":"1","month":"07","volume":13,"date_updated":"2026-06-18T19:41:34Z","publication_status":"published","oa":1,"acknowledgement":"We apologize to all the authors whose scientific work could not be cited and discussed because of space restrictions. We thank Dr. Inge Verstraeten (ISTAustria) and Dr. Juan Carlos Montesinos-Lopez (ETH Zürich) for helpful suggestions. This work was supported by the DOC Fellowship Programme of the Austrian Academy of Sciences (25008) to C.A.","status":"public","external_id":{"pmid":["33558367"],"isi":["000692069100001"]},"date_published":"2021-07-01T00:00:00Z","article_number":"a039941","title":"Auxin-regulated lateral root organogenesis","publisher":"Cold Spring Harbor Laboratory Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"N. Cavallari, C. Artner, E. Benková, Cold Spring Harbor Perspectives in Biology 13 (2021).","mla":"Cavallari, Nicola, et al. “Auxin-Regulated Lateral Root Organogenesis.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 13, no. 7, a039941, Cold Spring Harbor Laboratory Press, 2021, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039941\">10.1101/cshperspect.a039941</a>.","chicago":"Cavallari, Nicola, Christina Artner, and Eva Benková. “Auxin-Regulated Lateral Root Organogenesis.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2021. <a href=\"https://doi.org/10.1101/cshperspect.a039941\">https://doi.org/10.1101/cshperspect.a039941</a>.","apa":"Cavallari, N., Artner, C., &#38; Benková, E. (2021). Auxin-regulated lateral root organogenesis. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a039941\">https://doi.org/10.1101/cshperspect.a039941</a>","ista":"Cavallari N, Artner C, Benková E. 2021. Auxin-regulated lateral root organogenesis. Cold Spring Harbor Perspectives in Biology. 13(7), a039941.","ieee":"N. Cavallari, C. Artner, and E. Benková, “Auxin-regulated lateral root organogenesis,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 13, no. 7. Cold Spring Harbor Laboratory Press, 2021.","ama":"Cavallari N, Artner C, Benková E. Auxin-regulated lateral root organogenesis. <i>Cold Spring Harbor Perspectives in Biology</i>. 2021;13(7). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039941\">10.1101/cshperspect.a039941</a>"},"author":[{"first_name":"Nicola","full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina"},{"first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"doi":"10.1101/cshperspect.a039941","pmid":1,"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors."}],"ddc":["580"],"department":[{"_id":"EvBe"}],"article_type":"original","project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","publication_identifier":{"issn":["1943-0264"]},"scopus_import":"1","issue":"7","corr_author":"1","_id":"9212","language":[{"iso":"eng"}],"intvolume":"        13","day":"01","year":"2021","date_created":"2021-03-01T10:08:32Z","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a039941","open_access":"1"}],"isi":1},{"article_processing_charge":"No","publication_identifier":{"eissn":["1096-035X"],"issn":["0003-4916"]},"issue":"4","scopus_import":"1","day":"01","_id":"9224","language":[{"iso":"eng"}],"intvolume":"       427","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1911.04501","open_access":"1"}],"date_created":"2021-03-07T23:01:25Z","year":"2021","volume":427,"date_updated":"2025-07-10T12:01:41Z","publication":"Annals of Physics","quality_controlled":"1","month":"04","arxiv":1,"publication_status":"published","oa":1,"author":[{"full_name":"Abanin, D. A.","first_name":"D. A.","last_name":"Abanin"},{"last_name":"Bardarson","first_name":"J. H.","full_name":"Bardarson, J. H."},{"last_name":"De Tomasi","first_name":"G.","full_name":"De Tomasi, G."},{"last_name":"Gopalakrishnan","first_name":"S.","full_name":"Gopalakrishnan, S."},{"first_name":"V.","full_name":"Khemani, V.","last_name":"Khemani"},{"last_name":"Parameswaran","first_name":"S. A.","full_name":"Parameswaran, S. A."},{"first_name":"F.","full_name":"Pollmann, F.","last_name":"Pollmann"},{"last_name":"Potter","full_name":"Potter, A. C.","first_name":"A. C."},{"first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Vasseur, R.","first_name":"R.","last_name":"Vasseur"}],"citation":{"ista":"Abanin DA, Bardarson JH, De Tomasi G, Gopalakrishnan S, Khemani V, Parameswaran SA, Pollmann F, Potter AC, Serbyn M, Vasseur R. 2021. Distinguishing localization from chaos: Challenges in finite-size systems. Annals of Physics. 427(4), 168415.","apa":"Abanin, D. A., Bardarson, J. H., De Tomasi, G., Gopalakrishnan, S., Khemani, V., Parameswaran, S. A., … Vasseur, R. (2021). Distinguishing localization from chaos: Challenges in finite-size systems. <i>Annals of Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aop.2021.168415\">https://doi.org/10.1016/j.aop.2021.168415</a>","ieee":"D. A. Abanin <i>et al.</i>, “Distinguishing localization from chaos: Challenges in finite-size systems,” <i>Annals of Physics</i>, vol. 427, no. 4. Elsevier, 2021.","ama":"Abanin DA, Bardarson JH, De Tomasi G, et al. Distinguishing localization from chaos: Challenges in finite-size systems. <i>Annals of Physics</i>. 2021;427(4). doi:<a href=\"https://doi.org/10.1016/j.aop.2021.168415\">10.1016/j.aop.2021.168415</a>","mla":"Abanin, D. A., et al. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” <i>Annals of Physics</i>, vol. 427, no. 4, 168415, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aop.2021.168415\">10.1016/j.aop.2021.168415</a>.","short":"D.A. Abanin, J.H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S.A. Parameswaran, F. Pollmann, A.C. Potter, M. Serbyn, R. Vasseur, Annals of Physics 427 (2021).","chicago":"Abanin, D. A., J. H. Bardarson, G. De Tomasi, S. Gopalakrishnan, V. Khemani, S. A. Parameswaran, F. Pollmann, A. C. Potter, Maksym Serbyn, and R. Vasseur. “Distinguishing Localization from Chaos: Challenges in Finite-Size Systems.” <i>Annals of Physics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aop.2021.168415\">https://doi.org/10.1016/j.aop.2021.168415</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","oa_version":"Preprint","doi":"10.1016/j.aop.2021.168415","status":"public","date_published":"2021-04-01T00:00:00Z","article_number":"168415","title":"Distinguishing localization from chaos: Challenges in finite-size systems","external_id":{"isi":["000634879800007"],"arxiv":["1911.04501"]},"article_type":"original","department":[{"_id":"MaSe"}],"abstract":[{"text":"We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter.","lang":"eng"}],"type":"journal_article"},{"date_updated":"2026-04-08T06:59:49Z","volume":111,"month":"02","quality_controlled":"1","publication":"Letters in Mathematical Physics","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC Grant Agreement No 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged. Open Access funding provided by Institute of Science and Technology (IST Austria)","has_accepted_license":"1","oa":1,"file_date_updated":"2021-03-09T11:44:34Z","publication_status":"published","doi":"10.1007/s11005-020-01350-5","oa_version":"Published Version","publisher":"Springer Nature","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Feliciangeli D, Rademacher SAE, Seiringer R. Persistence of the spectral gap for the Landau–Pekar equations. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-020-01350-5\">10.1007/s11005-020-01350-5</a>","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “Persistence of the spectral gap for the Landau–Pekar equations,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","apa":"Feliciangeli, D., Rademacher, S. A. E., &#38; Seiringer, R. (2021). Persistence of the spectral gap for the Landau–Pekar equations. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-020-01350-5\">https://doi.org/10.1007/s11005-020-01350-5</a>","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. 2021. Persistence of the spectral gap for the Landau–Pekar equations. Letters in Mathematical Physics. 111, 19.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “Persistence of the Spectral Gap for the Landau–Pekar Equations.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-020-01350-5\">https://doi.org/10.1007/s11005-020-01350-5</a>.","mla":"Feliciangeli, Dario, et al. “Persistence of the Spectral Gap for the Landau–Pekar Equations.” <i>Letters in Mathematical Physics</i>, vol. 111, 19, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-020-01350-5\">10.1007/s11005-020-01350-5</a>.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, Letters in Mathematical Physics 111 (2021)."},"author":[{"full_name":"Feliciangeli, Dario","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli"},{"orcid":"0000-0001-5059-4466","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira","first_name":"Simone Anna Elvira"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"}],"external_id":{"isi":["000617195700001"]},"date_published":"2021-02-11T00:00:00Z","title":"Persistence of the spectral gap for the Landau–Pekar equations","article_number":"19","status":"public","article_type":"original","abstract":[{"text":"The Landau–Pekar equations describe the dynamics of a strongly coupled polaron.\r\nHere, we provide a class of initial data for which the associated effective Hamiltonian\r\nhas a uniform spectral gap for all times. For such initial data, this allows us to extend the\r\nresults on the adiabatic theorem for the Landau–Pekar equations and their derivation\r\nfrom the Fröhlich model obtained in previous works to larger times.","lang":"eng"}],"type":"journal_article","department":[{"_id":"RoSe"}],"ddc":["510"],"article_processing_charge":"Yes (via OA deal)","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"scopus_import":"1","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"ec_funded":1,"_id":"9225","intvolume":"       111","language":[{"iso":"eng"}],"day":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_created":"2021-03-09T11:44:34Z","file_size":391205,"relation":"main_file","checksum":"ffbfe1aad623bce7ff529c207e343b53","content_type":"application/pdf","access_level":"open_access","file_name":"2021_LettersMathPhysics_Feliciangeli.pdf","file_id":"9232","success":1,"creator":"dernst","date_updated":"2021-03-09T11:44:34Z"}],"isi":1,"date_created":"2021-03-07T23:01:25Z","year":"2021"},{"conference":{"end_date":"2021-02-13","location":"Rupnagar, India","start_date":"2021-02-11","name":"CALDAM: Conference on Algorithms and Discrete Applied Mathematics"},"isi":1,"year":"2021","date_created":"2021-03-07T23:01:25Z","language":[{"iso":"eng"}],"_id":"9227","intvolume":"     12601","day":"28","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030678982"]},"scopus_import":"1","article_processing_charge":"No","alternative_title":["LNCS"],"page":"346-358","type":"conference","abstract":[{"lang":"eng","text":"In the multiway cut problem we are given a weighted undirected graph   G=(V,E)  and a set   T⊆V  of k terminals. The goal is to find a minimum weight set of edges   E′⊆E  with the property that by removing   E′  from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio   2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem."}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","citation":{"short":"A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358.","mla":"Bloch-Hansen, Andrew, et al. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” <i>Conference on Algorithms and Discrete Applied Mathematics</i>, vol. 12601, Springer Nature, 2021, pp. 346–58, doi:<a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">10.1007/978-3-030-67899-9_28</a>.","chicago":"Bloch-Hansen, Andrew, Nasim Samei, and Roberto Solis-Oba. “Experimental Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.” In <i>Conference on Algorithms and Discrete Applied Mathematics</i>, 12601:346–58. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">https://doi.org/10.1007/978-3-030-67899-9_28</a>.","ieee":"A. Bloch-Hansen, N. Samei, and R. Solis-Oba, “Experimental evaluation of a local search approximation algorithm for the multiway cut problem,” in <i>Conference on Algorithms and Discrete Applied Mathematics</i>, Rupnagar, India, 2021, vol. 12601, pp. 346–358.","ista":"Bloch-Hansen A, Samei N, Solis-Oba R. 2021. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. Conference on Algorithms and Discrete Applied Mathematics. CALDAM: Conference on Algorithms and Discrete Applied Mathematics, LNCS, vol. 12601, 346–358.","apa":"Bloch-Hansen, A., Samei, N., &#38; Solis-Oba, R. (2021). Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In <i>Conference on Algorithms and Discrete Applied Mathematics</i> (Vol. 12601, pp. 346–358). Rupnagar, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">https://doi.org/10.1007/978-3-030-67899-9_28</a>","ama":"Bloch-Hansen A, Samei N, Solis-Oba R. Experimental evaluation of a local search approximation algorithm for the multiway cut problem. In: <i>Conference on Algorithms and Discrete Applied Mathematics</i>. Vol 12601. Springer Nature; 2021:346-358. doi:<a href=\"https://doi.org/10.1007/978-3-030-67899-9_28\">10.1007/978-3-030-67899-9_28</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Bloch-Hansen","full_name":"Bloch-Hansen, Andrew","first_name":"Andrew"},{"last_name":"Samei","id":"C1531CAE-36E9-11EA-845F-33AA3DDC885E","first_name":"Nasim","full_name":"Samei, Nasim"},{"full_name":"Solis-Oba, Roberto","first_name":"Roberto","last_name":"Solis-Oba"}],"doi":"10.1007/978-3-030-67899-9_28","oa_version":"None","status":"public","external_id":{"isi":["001433483100028"]},"title":"Experimental evaluation of a local search approximation algorithm for the multiway cut problem","date_published":"2021-01-28T00:00:00Z","publication_status":"published","volume":12601,"date_updated":"2025-09-10T10:01:54Z","publication":"Conference on Algorithms and Discrete Applied Mathematics","month":"01","quality_controlled":"1"},{"article_processing_charge":"No","issue":"4","scopus_import":"1","publication_identifier":{"issn":["1364-6613"],"eissn":["1879-307X"]},"day":"01","language":[{"iso":"eng"}],"_id":"9228","intvolume":"        25","file":[{"date_updated":"2022-05-27T07:31:24Z","success":1,"file_id":"11415","creator":"dernst","file_name":"2021_TrendsCognitiveSciences_Achakulvisut.pdf","content_type":"application/pdf","checksum":"87e39ea7bd266b976e8631b66979214d","access_level":"open_access","relation":"main_file","date_created":"2022-05-27T07:31:24Z","file_size":380720}],"year":"2021","date_created":"2021-03-07T23:01:25Z","isi":1,"month":"04","quality_controlled":"1","publication":"Trends in Cognitive Sciences","date_updated":"2023-08-07T13:59:07Z","volume":25,"file_date_updated":"2022-05-27T07:31:24Z","oa":1,"publication_status":"published","acknowledgement":"We thank all of our volunteers from the NMC conferences (list of names in the appendix). We also thank the NSF for support from 1734220 to B.W., and DARPA for support to T.A.","has_accepted_license":"1","title":"Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences","date_published":"2021-04-01T00:00:00Z","external_id":{"isi":["000627418000001"],"pmid":["33608214"]},"status":"public","oa_version":"Submitted Version","doi":"10.1016/j.tics.2021.01.007","pmid":1,"author":[{"last_name":"Achakulvisut","full_name":"Achakulvisut, Titipat","first_name":"Titipat"},{"last_name":"Ruangrong","full_name":"Ruangrong, Tulakan","first_name":"Tulakan"},{"last_name":"Mineault","full_name":"Mineault, Patrick","first_name":"Patrick"},{"first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels"},{"last_name":"Peters","full_name":"Peters, Megan A.K.","first_name":"Megan A.K."},{"first_name":"Panayiota","full_name":"Poirazi, Panayiota","last_name":"Poirazi"},{"first_name":"Christopher","full_name":"Rozell, Christopher","last_name":"Rozell"},{"first_name":"Brad","full_name":"Wyble, Brad","last_name":"Wyble"},{"full_name":"Goodman, Dan F.M.","first_name":"Dan F.M.","last_name":"Goodman"},{"last_name":"Kording","full_name":"Kording, Konrad Paul","first_name":"Konrad Paul"}],"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels, Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M. Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” <i>Trends in Cognitive Sciences</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">https://doi.org/10.1016/j.tics.2021.01.007</a>.","short":"T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P. Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive Sciences 25 (2021) 265–268.","mla":"Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” <i>Trends in Cognitive Sciences</i>, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:<a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">10.1016/j.tics.2021.01.007</a>.","ama":"Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. <i>Trends in Cognitive Sciences</i>. 2021;25(4):265-268. doi:<a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">10.1016/j.tics.2021.01.007</a>","apa":"Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A. K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. <i>Trends in Cognitive Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tics.2021.01.007\">https://doi.org/10.1016/j.tics.2021.01.007</a>","ista":"Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P, Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 25(4), 265–268.","ieee":"T. Achakulvisut <i>et al.</i>, “Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences,” <i>Trends in Cognitive Sciences</i>, vol. 25, no. 4. Elsevier, pp. 265–268, 2021."},"ddc":["570"],"department":[{"_id":"TiVo"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned."}],"article_type":"original","page":"265-268"},{"arxiv":1,"month":"03","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publication":"arXiv","date_updated":"2025-04-14T07:43:51Z","article_processing_charge":"No","oa":1,"ec_funded":1,"publication_status":"submitted","acknowledgement":"The research of L.-P. A. is supported in part by the grant NSF CAREER DMS-1653602. G. D. gratefully acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The research of L. H. is supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through Project-ID 233630050 -TRR 146, Project-ID 443891315 within SPP 2265 and Project-ID 446173099.","external_id":{"arxiv":["2103.04817"]},"date_published":"2021-03-08T00:00:00Z","title":"Maxima of a random model of the Riemann zeta function over intervals of varying length","article_number":"2103.04817","status":"public","language":[{"iso":"eng"}],"_id":"9230","doi":"10.48550/arXiv.2103.04817","oa_version":"Preprint","day":"08","citation":{"mla":"Arguin, Louis-Pierre, et al. “Maxima of a Random Model of the Riemann Zeta Function over Intervals of Varying Length.” <i>ArXiv</i>, 2103.04817, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.04817\">10.48550/arXiv.2103.04817</a>.","short":"L.-P. Arguin, G. Dubach, L. Hartung, ArXiv (n.d.).","chicago":"Arguin, Louis-Pierre, Guillaume Dubach, and Lisa Hartung. “Maxima of a Random Model of the Riemann Zeta Function over Intervals of Varying Length.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.04817\">https://doi.org/10.48550/arXiv.2103.04817</a>.","apa":"Arguin, L.-P., Dubach, G., &#38; Hartung, L. (n.d.). Maxima of a random model of the Riemann zeta function over intervals of varying length. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.04817\">https://doi.org/10.48550/arXiv.2103.04817</a>","ista":"Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta function over intervals of varying length. arXiv, 2103.04817.","ieee":"L.-P. Arguin, G. Dubach, and L. Hartung, “Maxima of a random model of the Riemann zeta function over intervals of varying length,” <i>arXiv</i>. .","ama":"Arguin L-P, Dubach G, Hartung L. Maxima of a random model of the Riemann zeta function over intervals of varying length. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.04817\">10.48550/arXiv.2103.04817</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Arguin","full_name":"Arguin, Louis-Pierre","first_name":"Louis-Pierre"},{"orcid":"0000-0001-6892-8137","last_name":"Dubach","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","full_name":"Dubach, Guillaume","first_name":"Guillaume"},{"full_name":"Hartung, Lisa","first_name":"Lisa","last_name":"Hartung"}],"type":"preprint","abstract":[{"lang":"eng","text":"We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate.\r\nIt is shown that the deterministic level of the maximum interpolates smoothly between the ones\r\nof log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from\r\n3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of\r\nlog-correlated variables with time-dependent variance and rate occur. A key ingredient of the\r\nproof is a precise upper tail tightness estimate for the maximum of the model on intervals of\r\nsize one, that includes a Gaussian correction. This correction is expected to be present for the\r\nRiemann zeta function and pertains to the question of the correct order of the maximum of\r\nthe zeta function in large intervals."}],"department":[{"_id":"LaEr"}],"year":"2021","date_created":"2021-03-09T11:08:15Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.04817"}]},{"day":"01","keyword":["Computer Networks and Communications","Software","Artificial Intelligence"],"_id":"9234","language":[{"iso":"eng"}],"intvolume":"        21","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"success":1,"creator":"kschuh","file_id":"9884","date_updated":"2021-08-11T12:44:16Z","file_name":"2021_NetworksSpatialEconomics_Shehu.pdf","content_type":"application/pdf","checksum":"22b4253a2e5da843622a2df713784b4c","access_level":"open_access","file_size":834964,"date_created":"2021-08-11T12:44:16Z","relation":"main_file"}],"isi":1,"year":"2021","date_created":"2021-03-10T12:18:47Z","article_processing_charge":"Yes (via OA deal)","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"issue":"2","scopus_import":"1","publication_identifier":{"eissn":["1572-9427"],"issn":["1566-113X"]},"ec_funded":1,"oa_version":"Published Version","doi":"10.1007/s11067-021-09517-w","author":[{"first_name":"Chinedu","full_name":"Izuchukwu, Chinedu","last_name":"Izuchukwu"},{"first_name":"Yekini","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"}],"citation":{"chicago":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” <i>Networks and Spatial Economics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11067-021-09517-w\">https://doi.org/10.1007/s11067-021-09517-w</a>.","mla":"Izuchukwu, Chinedu, and Yekini Shehu. “New Inertial Projection Methods for Solving Multivalued Variational Inequality Problems beyond Monotonicity.” <i>Networks and Spatial Economics</i>, vol. 21, no. 2, Springer Nature, 2021, pp. 291–323, doi:<a href=\"https://doi.org/10.1007/s11067-021-09517-w\">10.1007/s11067-021-09517-w</a>.","short":"C. Izuchukwu, Y. Shehu, Networks and Spatial Economics 21 (2021) 291–323.","ama":"Izuchukwu C, Shehu Y. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. <i>Networks and Spatial Economics</i>. 2021;21(2):291-323. doi:<a href=\"https://doi.org/10.1007/s11067-021-09517-w\">10.1007/s11067-021-09517-w</a>","ieee":"C. Izuchukwu and Y. Shehu, “New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity,” <i>Networks and Spatial Economics</i>, vol. 21, no. 2. Springer Nature, pp. 291–323, 2021.","ista":"Izuchukwu C, Shehu Y. 2021. New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. Networks and Spatial Economics. 21(2), 291–323.","apa":"Izuchukwu, C., &#38; Shehu, Y. (2021). New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity. <i>Networks and Spatial Economics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11067-021-09517-w\">https://doi.org/10.1007/s11067-021-09517-w</a>"},"publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2021-06-01T00:00:00Z","title":"New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity","external_id":{"isi":["000625002100001"]},"status":"public","article_type":"original","page":"291-323","ddc":["510"],"department":[{"_id":"VlKo"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps."}],"date_updated":"2024-11-04T13:52:33Z","volume":21,"quality_controlled":"1","month":"06","publication":"Networks and Spatial Economics","has_accepted_license":"1","acknowledgement":"The authors sincerely thank the Editor-in-Chief and anonymous referees for their careful reading, constructive comments and fruitful suggestions that help improve the manuscript. The research of the first author is supported by the National Research Foundation (NRF) South Africa (S& F-DSI/NRF Free Standing Postdoctoral Fellowship; Grant Number: 120784). The first author also acknowledges the financial support from DSI/NRF, South Africa Center of Excellence in Mathematical and Statistical Sciences (CoE-MaSS) Postdoctoral Fellowship. The second author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160). Open Access funding provided by Institute of Science and Technology (IST Austria).","file_date_updated":"2021-08-11T12:44:16Z","oa":1,"publication_status":"published"},{"issue":"8","scopus_import":"1","publication_identifier":{"issn":["0022-0000"],"eissn":["1090-2724"]},"article_processing_charge":"No","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.03835","open_access":"1"}],"year":"2021","date_created":"2021-03-14T23:01:32Z","day":"03","intvolume":"       119","_id":"9239","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6884"}]},"oa":1,"publication_status":"published","date_updated":"2025-07-10T11:53:57Z","volume":119,"quality_controlled":"1","month":"03","arxiv":1,"publication":"Journal of Computer and System Sciences","article_type":"original","page":"133-144","department":[{"_id":"ToHe"}],"abstract":[{"text":"A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion  to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","doi":"10.1016/j.jcss.2021.02.008","author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Đorđe","full_name":"Žikelić, Đorđe","last_name":"Žikelić"}],"citation":{"ieee":"G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,” <i>Journal of Computer and System Sciences</i>, vol. 119, no. 8. Elsevier, pp. 133–144, 2021.","apa":"Avni, G., Henzinger, T. A., &#38; Žikelić, Đ. (2021). Bidding mechanisms in graph games. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">https://doi.org/10.1016/j.jcss.2021.02.008</a>","ista":"Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 119(8), 133–144.","ama":"Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. <i>Journal of Computer and System Sciences</i>. 2021;119(8):133-144. doi:<a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">10.1016/j.jcss.2021.02.008</a>","mla":"Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” <i>Journal of Computer and System Sciences</i>, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:<a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">10.1016/j.jcss.2021.02.008</a>.","short":"G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144.","chicago":"Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in Graph Games.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jcss.2021.02.008\">https://doi.org/10.1016/j.jcss.2021.02.008</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","title":"Bidding mechanisms in graph games","date_published":"2021-03-03T00:00:00Z","external_id":{"arxiv":["1905.03835"],"isi":["000634149800009"]},"status":"public"},{"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"issue":"5","scopus_import":"1","publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"day":"25","intvolume":"       284","_id":"9240","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_created":"2021-03-22T07:18:01Z","file_size":473310,"relation":"main_file","checksum":"c630b691fb9e716b02aa6103a9794ec8","content_type":"application/pdf","access_level":"open_access","file_name":"2021_JourDiffEquations_Cornalba.pdf","file_id":"9267","success":1,"creator":"dernst","date_updated":"2021-03-22T07:18:01Z"}],"date_created":"2021-03-14T23:01:32Z","year":"2021","isi":1,"month":"05","quality_controlled":"1","publication":"Journal of Differential Equations","date_updated":"2025-04-14T07:43:51Z","volume":284,"file_date_updated":"2021-03-22T07:18:01Z","oa":1,"publication_status":"published","acknowledgement":"All authors thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. This paper was motivated by stimulating discussions at the First Berlin–Leipzig Workshop on Fluctuating Hydrodynamics in August 2019 with Ana Djurdjevac, Rupert Klein and Ralf Kornhuber. JZ gratefully acknowledges funding by a Royal Society Wolfson Research Merit Award. FC gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","has_accepted_license":"1","title":"Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions","date_published":"2021-05-25T00:00:00Z","external_id":{"isi":["000634823300010"]},"status":"public","oa_version":"Published Version","doi":"10.1016/j.jde.2021.02.048","author":[{"full_name":"Cornalba, Federico","first_name":"Federico","last_name":"Cornalba","id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149"},{"first_name":"Tony","full_name":"Shardlow, Tony","last_name":"Shardlow"},{"last_name":"Zimmer","full_name":"Zimmer, Johannes","first_name":"Johannes"}],"publisher":"Elsevier","citation":{"ama":"Cornalba F, Shardlow T, Zimmer J. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. <i>Journal of Differential Equations</i>. 2021;284(5):253-283. doi:<a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">10.1016/j.jde.2021.02.048</a>","apa":"Cornalba, F., Shardlow, T., &#38; Zimmer, J. (2021). Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">https://doi.org/10.1016/j.jde.2021.02.048</a>","ista":"Cornalba F, Shardlow T, Zimmer J. 2021. Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions. Journal of Differential Equations. 284(5), 253–283.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions,” <i>Journal of Differential Equations</i>, vol. 284, no. 5. Elsevier, pp. 253–283, 2021.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” <i>Journal of Differential Equations</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">https://doi.org/10.1016/j.jde.2021.02.048</a>.","mla":"Cornalba, Federico, et al. “Well-Posedness for a Regularised Inertial Dean–Kawasaki Model for Slender Particles in Several Space Dimensions.” <i>Journal of Differential Equations</i>, vol. 284, no. 5, Elsevier, 2021, pp. 253–83, doi:<a href=\"https://doi.org/10.1016/j.jde.2021.02.048\">10.1016/j.jde.2021.02.048</a>.","short":"F. Cornalba, T. Shardlow, J. Zimmer, Journal of Differential Equations 284 (2021) 253–283."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["510"],"department":[{"_id":"JuFi"}],"type":"journal_article","abstract":[{"text":"A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to  for  and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula.","lang":"eng"}],"article_type":"original","page":"253-283"},{"date_updated":"2023-08-07T14:11:18Z","volume":103,"month":"02","quality_controlled":"1","arxiv":1,"publication":"Physical Review A","acknowledgement":"I thank Prof. Shabir Barzanjeh and Dr. Ulrich Vogl for the fruitful discussions.\r\n","oa":1,"publication_status":"published","oa_version":"Preprint","doi":"10.1103/PhysRevA.103.023708","author":[{"orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R"}],"citation":{"chicago":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>.","short":"A.R. Rueda Sanchez, Physical Review A 103 (2021).","mla":"Rueda Sanchez, Alfredo R. “Frequency-Multiplexed Hybrid Optical Entangled Source Based on the Pockels Effect.” <i>Physical Review A</i>, vol. 103, no. 2, 023708, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>.","ama":"Rueda Sanchez AR. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. 2021;103(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">10.1103/PhysRevA.103.023708</a>","ista":"Rueda Sanchez AR. 2021. Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. Physical Review A. 103(2), 023708.","apa":"Rueda Sanchez, A. R. (2021). Frequency-multiplexed hybrid optical entangled source based on the Pockels effect. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.023708\">https://doi.org/10.1103/PhysRevA.103.023708</a>","ieee":"A. R. Rueda Sanchez, “Frequency-multiplexed hybrid optical entangled source based on the Pockels effect,” <i>Physical Review A</i>, vol. 103, no. 2. American Physical Society, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","date_published":"2021-02-11T00:00:00Z","title":"Frequency-multiplexed hybrid optical entangled source based on the Pockels effect","article_number":"023708","external_id":{"arxiv":["2010.05356"],"isi":["000617037900013"]},"status":"public","article_type":"original","department":[{"_id":"JoFi"}],"type":"journal_article","abstract":[{"text":"In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing.","lang":"eng"}],"article_processing_charge":"No","issue":"2","scopus_import":"1","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"day":"11","_id":"9242","intvolume":"       103","language":[{"iso":"eng"}],"isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2010.05356","open_access":"1"}],"year":"2021","date_created":"2021-03-14T23:01:33Z"},{"ddc":["570"],"department":[{"_id":"MaLo"}],"type":"journal_article","abstract":[{"text":"Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.","lang":"eng"}],"article_type":"original","status":"public","date_published":"2021-02-24T00:00:00Z","article_number":"1-32","title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","external_id":{"isi":["000627596400001"]},"author":[{"last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M."},{"first_name":"Natalia S.","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"last_name":"Peters","full_name":"Peters, Katharina","first_name":"Katharina"},{"first_name":"Eefjan","full_name":"Breukink, Eefjan","last_name":"Breukink"},{"first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"}],"publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>, vol. 10, 1–32, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>.","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021).","chicago":"Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>.","ieee":"V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose, and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose, M., &#38; Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>","ista":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 10, 1–32.","ama":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>"},"oa_version":"Published Version","doi":"10.7554/eLife.61525","publication_status":"published","file_date_updated":"2021-03-22T07:36:08Z","oa":1,"acknowledgement":"We thank Alexander Egan (Newcastle University) for purified proteins LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM, and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge Christian P Richter and Changjiang You (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). ","has_accepted_license":"1","publication":"eLife","quality_controlled":"1","month":"02","volume":10,"date_updated":"2024-10-22T10:04:21Z","year":"2021","date_created":"2021-03-14T23:01:33Z","isi":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_created":"2021-03-22T07:36:08Z","file_size":2314698,"relation":"main_file","content_type":"application/pdf","checksum":"79897a09bfecd9914d39c4aea2841855","access_level":"open_access","file_name":"2021_eLife_HernandezRocamora.pdf","file_id":"9268","success":1,"creator":"dernst","date_updated":"2021-03-22T07:36:08Z"}],"day":"24","language":[{"iso":"eng"}],"_id":"9243","intvolume":"        10","ec_funded":1,"publication_identifier":{"eissn":["2050-084X"]},"scopus_import":"1","project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis"}],"article_processing_charge":"No"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","date_created":"2021-03-22T08:50:33Z","file_size":9259690,"relation":"main_file","success":1,"file_id":"9271","creator":"dernst","date_updated":"2021-03-22T08:50:33Z","file_name":"2021_eLife_Hankeova.pdf"}],"day":"26","intvolume":"        10","_id":"9244","language":[{"iso":"eng"}],"year":"2021","date_created":"2021-03-14T23:01:34Z","isi":1,"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"article_processing_charge":"No","ec_funded":1,"publication_identifier":{"eissn":["2050-084X"]},"scopus_import":"1","status":"public","date_published":"2021-02-26T00:00:00Z","article_number":"e60916","title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","external_id":{"pmid":["33635272"],"isi":["000625357100001"]},"author":[{"last_name":"Hankeova","first_name":"Simona","full_name":"Hankeova, Simona"},{"full_name":"Salplachta, Jakub","first_name":"Jakub","last_name":"Salplachta"},{"last_name":"Zikmund","full_name":"Zikmund, Tomas","first_name":"Tomas"},{"last_name":"Kavkova","first_name":"Michaela","full_name":"Kavkova, Michaela"},{"last_name":"Van Hul","first_name":"Noémi","full_name":"Van Hul, Noémi"},{"last_name":"Brinek","full_name":"Brinek, Adam","first_name":"Adam"},{"full_name":"Smekalova, Veronika","first_name":"Veronika","last_name":"Smekalova"},{"last_name":"Laznovsky","full_name":"Laznovsky, Jakub","first_name":"Jakub"},{"first_name":"Feven","full_name":"Dawit, Feven","last_name":"Dawit"},{"last_name":"Jaros","full_name":"Jaros, Josef","first_name":"Josef"},{"first_name":"Vítězslav","full_name":"Bryja, Vítězslav","last_name":"Bryja"},{"first_name":"Urban","full_name":"Lendahl, Urban","last_name":"Lendahl"},{"last_name":"Ellis","first_name":"Ewa","full_name":"Ellis, Ewa"},{"full_name":"Nemeth, Antal","first_name":"Antal","last_name":"Nemeth"},{"last_name":"Fischler","full_name":"Fischler, Björn","first_name":"Björn"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"first_name":"Emma Rachel","full_name":"Andersson, Emma Rachel","last_name":"Andersson"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"eLife Sciences Publications","citation":{"short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>, vol. 10, e60916, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>.","chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>.","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>","ieee":"S. Hankeova <i>et al.</i>, “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>"},"oa_version":"Published Version","doi":"10.7554/eLife.60916","pmid":1,"ddc":["570"],"department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models."}],"type":"journal_article","article_type":"original","publication":"eLife","month":"02","quality_controlled":"1","volume":10,"date_updated":"2026-04-02T14:00:00Z","publication_status":"published","file_date_updated":"2021-03-22T08:50:33Z","oa":1,"has_accepted_license":"1","acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.)."}]