[{"publication_identifier":{"issn":["1553-7358"]},"month":"02","doi":"10.1371/journal.pcbi.1007642","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000526725200019"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:48:00Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e1007642","related_material":{"record":[{"id":"9716","relation":"research_data","status":"deleted"},{"status":"public","relation":"research_data","id":"9776"},{"status":"public","relation":"used_in_publication","id":"9779"},{"status":"public","relation":"dissertation_contains","id":"8155"},{"id":"9777","status":"public","relation":"research_data"}]},"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"volume":16,"date_created":"2020-03-06T07:39:38Z","date_updated":"2023-09-12T11:02:24Z","year":"2020","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":"1","date_published":"2020-02-25T00:00:00Z","citation":{"ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020)."},"publication":"PLOS Computational Biology","article_type":"original","issue":"2","abstract":[{"text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_PlosCompBio_Grah.pdf","file_size":2209325,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7579","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-09T15:12:21Z"}],"oa_version":"Published Version","_id":"7569","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 16","ddc":["000","570"],"title":"The relation between crosstalk and gene regulation form revisited","status":"public"},{"publication":"bioRxiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.03.366948"}],"citation":{"ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948."},"oa":1,"external_id":{"pmid":["PPR234457 "]},"date_published":"2020-11-05T00:00:00Z","doi":"10.1101/2020.11.03.366948","language":[{"iso":"eng"}],"month":"11","day":"05","article_processing_charge":"No","year":"2020","_id":"8813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"status":"public","publication_status":"submitted","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","department":[{"_id":"SiHi"}],"publisher":"Cold Spring Harbor Laboratory","author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"last_name":"Halbritter","first_name":"Florian","full_name":"Halbritter, Florian"},{"last_name":"Titz-Teixeira","first_name":"Fabian","full_name":"Titz-Teixeira, Fabian"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","first_name":"Julia","last_name":"Ramesmayer"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"last_name":"Warr","first_name":"Nick","full_name":"Warr, Nick"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"full_name":"Farlik, Matthias","first_name":"Matthias","last_name":"Farlik"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","last_name":"Perry","first_name":"Anthony C. F."},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"date_updated":"2023-09-12T11:05:28Z","date_created":"2020-11-26T07:17:19Z","oa_version":"Preprint","type":"preprint","abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}]},{"type":"research_data_reference","date_updated":"2023-09-12T11:02:25Z","date_created":"2021-08-06T07:21:51Z","oa_version":"None","author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7569"}]},"status":"public","title":"Maximizing crosstalk","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9777","year":"2020","day":"25","month":"02","article_processing_charge":"No","doi":"10.1371/journal.pcbi.1007642.s002","date_published":"2020-02-25T00:00:00Z","oa":1,"citation":{"ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002.","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.","short":"R. Grah, T. Friedlander, (2020)."},"main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}]},{"publication_identifier":{"issn":["2663-337X"]},"month":"09","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"doi":"10.15479/AT:ISTA:8332","file_date_updated":"2020-09-04T13:00:17Z","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_updated":"2023-09-13T08:45:08Z","date_created":"2020-09-04T12:24:12Z","related_material":{"record":[{"id":"133","status":"public","relation":"part_of_dissertation"},{"id":"8012","relation":"part_of_dissertation","status":"public"},{"id":"8195","relation":"part_of_dissertation","status":"public"},{"id":"160","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard"}],"has_accepted_license":"1","article_processing_charge":"No","day":"03","page":"120","citation":{"short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria."},"date_published":"2020-09-03T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","_id":"8332","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"8333","checksum":"26fe261550f691280bda4c454bf015c7","date_updated":"2020-09-04T12:17:47Z","date_created":"2020-09-04T12:17:47Z","access_level":"open_access","file_name":"kragl-thesis.pdf","content_type":"application/pdf","file_size":1348815,"creator":"bkragl"},{"date_created":"2020-09-04T13:00:17Z","date_updated":"2020-09-04T13:00:17Z","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","relation":"source_file","creator":"bkragl","file_size":372312,"content_type":"application/zip","file_name":"kragl-thesis.zip","access_level":"closed"}],"oa_version":"Published Version"},{"publication_identifier":{"isbn":["9781713829546"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-01-01T00:00:00Z","conference":{"start_date":"2020-12-06","location":"Virtual","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems"},"page":"11525-11538","quality_controlled":"1","external_id":{"arxiv":["2006.15055"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2006.15055","open_access":"1"}],"citation":{"short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38.","chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020.","ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538.","apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.","ieee":"F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538.","ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538."},"oa":1,"publication":"Advances in Neural Information Processing Systems","extern":"1","abstract":[{"text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n","lang":"eng"}],"type":"conference","oa_version":"Preprint","volume":33,"date_updated":"2023-09-13T12:19:19Z","date_created":"2023-09-13T12:03:46Z","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Weissenborn, Dirk","first_name":"Dirk","last_name":"Weissenborn"},{"first_name":"Thomas","last_name":"Unterthiner","full_name":"Unterthiner, Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"last_name":"Heigold","first_name":"Georg","full_name":"Heigold, Georg"},{"last_name":"Uszkoreit","first_name":"Jakob","full_name":"Uszkoreit, Jakob"},{"full_name":"Dosovitskiy, Alexey","last_name":"Dosovitskiy","first_name":"Alexey"},{"full_name":"Kipf, Thomas","last_name":"Kipf","first_name":"Thomas"}],"department":[{"_id":"FrLo"}],"publisher":"Curran Associates","intvolume":" 33","title":"Object-centric learning with slot attention","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14326","year":"2020"},{"oa_version":"Preprint","_id":"71","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 52","title":"Scaling limits of discrete optimal transport","status":"public","issue":"3","abstract":[{"lang":"eng","text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric."}],"type":"journal_article","date_published":"2020-10-01T00:00:00Z","citation":{"chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440"},"publication":"SIAM Journal on Mathematical Analysis","page":"2759-2802","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Gladbach, Peter","first_name":"Peter","last_name":"Gladbach"},{"full_name":"Kopfer, Eva","first_name":"Eva","last_name":"Kopfer"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"}],"volume":52,"date_created":"2018-12-11T11:44:28Z","date_updated":"2023-09-18T08:13:15Z","year":"2020","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JaMa"}],"publication_status":"published","publist_id":"7983","doi":"10.1137/19M1243440","language":[{"iso":"eng"}],"external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"month":"10"},{"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000532295600014"],"pmid":["30507534"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1109/TVCG.2018.2883628","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"month":"06","publisher":"IEEE","department":[{"_id":"ChWo"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","volume":26,"date_created":"2018-12-16T22:59:21Z","date_updated":"2023-09-18T09:30:01Z","author":[{"last_name":"Hikaru","first_name":"Ibayashi","full_name":"Hikaru, Ibayashi"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"file_date_updated":"2020-10-08T08:34:53Z","page":"2288-2302","article_type":"original","citation":{"mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628","ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020."},"publication":"IEEE Transactions on Visualization and Computer Graphics","date_published":"2020-06-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 26","status":"public","ddc":["006"],"title":"Simulating liquids on dynamically warping grids","_id":"5681","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"creator":"wojtan","file_size":21910098,"content_type":"application/pdf","access_level":"open_access","file_name":"preprint.pdf","success":1,"checksum":"8d4c55443a0ee335bb5bb652de503042","date_updated":"2020-10-08T08:34:53Z","date_created":"2020-10-08T08:34:53Z","file_id":"8626","relation":"main_file"}],"type":"journal_article","issue":"6","abstract":[{"text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.","lang":"eng"}]},{"doi":"10.15479/AT:ISTA:8958","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"oa":1,"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"publication_identifier":{"issn":["2663-337X"]},"month":"12","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5886"},{"id":"8587","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1120"}]},"author":[{"full_name":"Li, Xiang","first_name":"Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-12-21T09:44:30Z","date_updated":"2023-09-20T11:30:58Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-12-30T07:18:03Z","date_published":"2020-12-21T00:00:00Z","citation":{"ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020."},"page":"125","article_processing_charge":"No","has_accepted_license":"1","day":"21","oa_version":"Published Version","file":[{"file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3622305,"creator":"xli","relation":"main_file","file_id":"8967","date_created":"2020-12-22T10:55:56Z","date_updated":"2020-12-22T10:55:56Z","checksum":"3994c54a1241451d561db1d4f43bad30","success":1},{"file_name":"THESIS_Xiang_Li.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":4018859,"creator":"xli","relation":"source_file","file_id":"8968","date_created":"2020-12-22T10:56:03Z","date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8958","ddc":["539"],"status":"public","title":"Rotation of coupled cold molecules in the presence of a many-body environment","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"date_published":"2020-09-14T00:00:00Z","page":"148","citation":{"mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386"},"day":"14","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"file_name":"Thesis_Ran.zip","access_level":"closed","file_size":1245800191,"content_type":"application/x-zip-compressed","creator":"rzhang","relation":"source_file","file_id":"8388","date_created":"2020-09-14T01:02:59Z","date_updated":"2020-09-14T12:18:43Z","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba"},{"date_updated":"2020-09-15T12:51:53Z","date_created":"2020-09-15T12:51:53Z","checksum":"817e20c33be9247f906925517c56a40d","success":1,"relation":"main_file","file_id":"8396","content_type":"application/pdf","file_size":161385316,"creator":"rzhang","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","access_level":"open_access"}],"ddc":["003"],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","status":"public","_id":"8386","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","supervisor":[{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8386","project":[{"name":"Distributed 3D Object Design","call_identifier":"H2020","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]},"date_created":"2020-09-14T01:04:53Z","date_updated":"2023-09-22T09:49:31Z","author":[{"last_name":"Zhang","first_name":"Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran"}],"related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"id":"1002","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"year":"2020","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","file_date_updated":"2020-09-15T12:51:53Z","ec_funded":1},{"publication_identifier":{"issn":["2663-337X"]},"month":"06","doi":"10.15479/AT:ISTA:7996","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"oa":1,"file_date_updated":"2020-07-14T12:48:07Z","related_material":{"record":[{"id":"1328","relation":"part_of_dissertation","status":"public"},{"id":"7541","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"77"},{"id":"23","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"840"}]},"author":[{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip"}],"date_created":"2020-06-22T09:22:23Z","date_updated":"2023-09-26T15:50:22Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"22","date_published":"2020-06-22T00:00:00Z","citation":{"short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria."},"page":"178","abstract":[{"text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"checksum":"467e52feb3e361ce8cf5fe8d5c254ece","date_updated":"2020-07-14T12:48:07Z","date_created":"2020-06-22T09:22:04Z","file_id":"7997","relation":"main_file","creator":"dernst","content_type":"application/x-zip-compressed","file_size":392794743,"access_level":"closed","file_name":"JK_thesis_latex_source_files.zip"},{"checksum":"1de716bf110dbd77d383e479232bf496","date_updated":"2020-07-14T12:48:07Z","date_created":"2020-06-22T09:21:29Z","file_id":"7998","relation":"main_file","creator":"dernst","file_size":28453247,"content_type":"application/pdf","access_level":"open_access","file_name":"PhD_thesis_JK_pdfa.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7996","ddc":["530"],"status":"public","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing"},{"publication_identifier":{"issn":["03029743"],"isbn":["9783030532901"],"eissn":["16113349"]},"month":"07","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-53291-8_21","conference":{"name":"CAV: Computer Aided Verification"},"ec_funded":1,"file_date_updated":"2020-08-17T11:32:44Z","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","volume":12225,"date_created":"2020-08-16T22:00:58Z","date_updated":"2023-10-03T11:36:13Z","related_material":{"record":[{"id":"12738","status":"public","relation":"later_version"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen","full_name":"Katoen, Joost P"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"full_name":"Winkler, Tobias","first_name":"Tobias","last_name":"Winkler"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"14","page":"398-420","citation":{"ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21."},"publication":"International Conference on Computer Aided Verification","date_published":"2020-07-14T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"intvolume":" 12225","status":"public","title":"Stochastic games with lexicographic reachability-safety objectives","ddc":["000"],"_id":"8272","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"8276","relation":"main_file","date_updated":"2020-08-17T11:32:44Z","date_created":"2020-08-17T11:32:44Z","success":1,"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","file_name":"2020_LNCS_CAV_Chatterjee.pdf","access_level":"open_access","creator":"dernst","file_size":625056,"content_type":"application/pdf"}]},{"month":"02","publication_identifier":{"issn":["0091679X"]},"isi":1,"quality_controlled":"1","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"external_id":{"isi":["000611826500008"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2020.01.006","ec_funded":1,"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","editor":[{"first_name":"Phong ","last_name":"Tran","full_name":"Tran, Phong "}],"year":"2020","date_created":"2020-03-08T23:00:47Z","date_updated":"2023-10-04T09:50:24Z","volume":158,"author":[{"full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","first_name":"Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"related_material":{"record":[{"id":"8358","status":"public","relation":"part_of_dissertation"}]},"scopus_import":"1","day":"27","article_processing_charge":"No","page":"145-161","publication":"Methods in Cell Biology","citation":{"short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161."},"date_published":"2020-02-27T00:00:00Z","alternative_title":["Methods in Cell Biology"],"type":"book_chapter","abstract":[{"text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.","lang":"eng"}],"status":"public","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","intvolume":" 158","_id":"7572","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7387","intvolume":" 5","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","status":"public","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2020-01-20T00:00:00Z","citation":{"ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5."},"publication":"Nature Microbiology","page":"407-417","article_type":"letter_note","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14280"}]},"author":[{"last_name":"Baranova","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S."},{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler"},{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"full_name":"Alfonso, Carlos","last_name":"Alfonso","first_name":"Carlos"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rivas, Germán","last_name":"Rivas","first_name":"Germán"},{"last_name":"Vollmer","first_name":"Waldemar","full_name":"Vollmer, Waldemar"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"}],"volume":5,"date_updated":"2023-10-06T12:22:38Z","date_created":"2020-01-28T16:14:41Z","pmid":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","year":"2020","publisher":"Springer Nature","department":[{"_id":"MaLo"}],"publication_status":"published","publication_identifier":{"issn":["2058-5276"]},"month":"01","doi":"10.1038/s41564-019-0657-5","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"external_id":{"isi":["000508584700007"],"pmid":["31959972"]},"oa":1,"project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163"}],"isi":1,"quality_controlled":"1"},{"department":[{"_id":"HeEd"}],"publisher":"Akadémiai Kiadó","publication_status":"published","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","year":"2020","volume":57,"date_updated":"2023-10-10T13:05:27Z","date_created":"2020-07-24T07:09:18Z","author":[{"last_name":"Vegter","first_name":"Gert","full_name":"Vegter, Gert"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-07-24T07:09:06Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000570978400005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1556/012.2020.57.2.1454","publication_identifier":{"eissn":["1588-2896"],"issn":["0081-6906"]},"month":"07","intvolume":" 57","ddc":["510"],"status":"public","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","_id":"8163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":1476072,"creator":"mwintrae","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","access_level":"open_access","date_updated":"2020-07-24T07:09:06Z","date_created":"2020-07-24T07:09:06Z","relation":"main_file","file_id":"8164"}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"page":"193-199","article_type":"original","citation":{"chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454"},"publication":"Studia Scientiarum Mathematicarum Hungarica","date_published":"2020-07-24T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24"},{"quality_controlled":"1","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"external_id":{"arxiv":["1805.10672"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.29252/ijmsi.15.2.117","month":"10","publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Iranian Academic Center for Education, Culture and Research","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","year":"2020","date_updated":"2023-10-16T09:25:00Z","date_created":"2020-10-18T22:01:36Z","volume":15,"author":[{"full_name":"Shakiba, A.","last_name":"Shakiba","first_name":"A."},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"full_name":"Hooshmandasl, M.R.","last_name":"Hooshmandasl","first_name":"M.R."},{"full_name":"Alambardar Meybodi, M.","first_name":"M.","last_name":"Alambardar Meybodi"}],"file_date_updated":"2020-10-19T11:14:20Z","article_type":"original","page":"117-128","publication":"Iranian Journal of Mathematical Sciences and Informatics","citation":{"ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117."},"date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","ddc":["000"],"status":"public","title":"A note on belief structures and s-approximation spaces","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8671","file":[{"creator":"dernst","content_type":"application/pdf","file_size":261688,"access_level":"open_access","file_name":"2020_ijmsi_Shakiba_accepted.pdf","success":1,"checksum":"f299661a6d51cda6d255a76be696f48d","date_updated":"2020-10-19T11:14:20Z","date_created":"2020-10-19T11:14:20Z","file_id":"8676","relation":"main_file"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ","lang":"eng"}],"issue":"2"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8549","checksum":"8e7c42e72596f6889d786e8e8b89994f","success":1,"date_updated":"2020-09-21T13:15:02Z","date_created":"2020-09-21T13:15:02Z","access_level":"open_access","file_name":"2020_EJournProbab_Dareiotis.pdf","content_type":"application/pdf","file_size":273042,"creator":"dernst"}],"intvolume":" 25","title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","ddc":["510"],"status":"public","_id":"6359","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients."}],"type":"journal_article","date_published":"2020-07-16T00:00:00Z","article_type":"original","citation":{"chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479.","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479"},"publication":"Electronic Journal of Probability","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","volume":25,"date_created":"2019-04-30T07:40:17Z","date_updated":"2023-10-16T09:22:50Z","author":[{"first_name":"Konstantinos","last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"}],"publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2020","file_date_updated":"2020-09-21T13:15:02Z","article_number":"82","language":[{"iso":"eng"}],"doi":"10.1214/20-EJP479","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"publication_identifier":{"eissn":["1083-6489"]},"month":"07"},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":30224591,"creator":"dernst","file_name":"2020_Thesis_Royer.pdf","access_level":"open_access","date_created":"2020-09-14T13:39:14Z","date_updated":"2020-09-14T13:39:14Z","checksum":"c914d2f88846032f3d8507734861b6ee","success":1,"relation":"main_file","file_id":"8391"},{"checksum":"ae98fb35d912cff84a89035ae5794d3c","date_created":"2020-09-14T13:39:17Z","date_updated":"2020-09-14T13:39:17Z","file_id":"8392","relation":"main_file","creator":"dernst","file_size":74227627,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"thesis_sources.zip"}],"_id":"8390","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","ddc":["000"],"status":"public","abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-14T00:00:00Z","citation":{"short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria."},"page":"197","has_accepted_license":"1","article_processing_charge":"No","day":"14","related_material":{"record":[{"id":"7936","relation":"part_of_dissertation","status":"public"},{"id":"7937","status":"public","relation":"part_of_dissertation"},{"id":"8193","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"id":"911","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"}],"date_created":"2020-09-14T13:42:09Z","date_updated":"2023-10-16T10:04:02Z","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","year":"2020","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2020-09-14T13:39:17Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.15479/AT:ISTA:8390","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"month":"09"},{"quality_controlled":"1","external_id":{"arxiv":["2004.04180"]},"main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2020-06-19","start_date":"2020-06-14","location":"Virtual"},"doi":"10.1109/CVPR42600.2020.00752","month":"07","publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}],"year":"2020","date_updated":"2023-10-17T07:37:11Z","date_created":"2020-07-31T16:53:49Z","author":[{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M"},{"full_name":"Tsiminaki, Vagia","first_name":"Vagia","last_name":"Tsiminaki"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"file_date_updated":"2020-07-31T16:57:12Z","page":"7498-7507","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","citation":{"chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752"},"date_published":"2020-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","title":"Leveraging 2D data to learn textured 3D mesh generation","status":"public","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8186","file":[{"file_name":"paper.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10262773,"creator":"phenders","relation":"main_file","file_id":"8187","date_updated":"2020-07-31T16:57:12Z","date_created":"2020-07-31T16:57:12Z","success":1}],"oa_version":"Submitted Version","type":"conference","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","citation":{"ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175.","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175."},"publication":"Plant Signaling & Behavior","article_type":"original","issue":"1","abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7416","intvolume":" 15","status":"public","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","publication_identifier":{"issn":["1559-2324"]},"month":"01","doi":"10.1080/15592324.2019.1687175","language":[{"iso":"eng"}],"external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"oa":1,"quality_controlled":"1","isi":1,"article_number":"1687175","author":[{"full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","last_name":"Sinclair","first_name":"Scott A"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"volume":15,"date_created":"2020-01-30T10:12:04Z","date_updated":"2023-10-17T09:01:48Z","pmid":1,"year":"2020","department":[{"_id":"JiFr"}],"publisher":"Taylor & Francis","publication_status":"published"},{"keyword":["General Mathematics"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"251-297","publication":"Studia Mathematica","citation":{"mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2.","short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297.","chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2.","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2","ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297.","apa":"Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020."},"date_published":"2020-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces."}],"issue":"3","title":"Modelled distributions of Triebel–Lizorkin type","status":"public","intvolume":" 252","_id":"9196","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"03","publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000558100500002"],"arxiv":["1709.05202"]},"language":[{"iso":"eng"}],"doi":"10.4064/sm180411-11-2","publication_status":"published","publisher":"Instytut Matematyczny","department":[{"_id":"JuFi"},{"_id":"GradSch"}],"year":"2020","date_created":"2021-02-25T08:55:03Z","date_updated":"2023-10-17T09:15:53Z","volume":252,"author":[{"last_name":"Hensel","first_name":"Sebastian","orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","full_name":"Hensel, Sebastian"},{"last_name":"Rosati","first_name":"Tommaso","full_name":"Rosati, Tommaso"}]},{"intvolume":" 16","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","ddc":["570"],"status":"public","_id":"7464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access","file_size":4551246,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7484","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","checksum":"a297f54d1fef0efe4789ca00f37f241e"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly."}],"article_type":"original","citation":{"short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277."},"publication":"PLOS Pathogens","date_published":"2020-01-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","department":[{"_id":"FlSc"}],"publisher":"Public Library of Science","publication_status":"published","pmid":1,"year":"2020","volume":16,"date_updated":"2023-10-17T12:29:34Z","date_created":"2020-02-06T18:47:17Z","related_material":{"record":[{"id":"9723","status":"deleted","relation":"research_data"}]},"author":[{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"last_name":"Morado","first_name":"Dustin R.","full_name":"Morado, Dustin R."},{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ricana, Clifton L.","first_name":"Clifton L.","last_name":"Ricana"},{"full_name":"Lyddon, Terri D.","last_name":"Lyddon","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"full_name":"Feathers, J. Ryan","last_name":"Feathers","first_name":"J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"article_number":"e1008277","file_date_updated":"2020-07-14T12:47:59Z","project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1371/journal.ppat.1008277","publication_identifier":{"issn":["1553-7374"]},"month":"01"},{"article_number":"e1007494","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7196"}]},"author":[{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"volume":16,"date_created":"2019-12-23T13:45:11Z","date_updated":"2023-10-17T12:29:47Z","publication_identifier":{"eissn":["15537358"]},"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1906.02785"],"isi":["000510916500025"]},"oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1007494","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7212","intvolume":" 16","ddc":["000"],"status":"public","title":"Limits on amplifiers of natural selection under death-Birth updating","oa_version":"Published Version","file":[{"checksum":"ce32ee2d2f53aed832f78bbd47e882df","date_created":"2020-02-03T07:32:42Z","date_updated":"2020-07-14T12:47:53Z","relation":"main_file","file_id":"7441","content_type":"application/pdf","file_size":1817531,"creator":"dernst","access_level":"open_access","file_name":"2020_PlosCompBio_Tkadlec.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"17","citation":{"mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494"},"publication":"PLoS computational biology","article_type":"original","date_published":"2020-01-17T00:00:00Z"},{"title":"A role of graphs in evolutionary processes","ddc":["519"],"status":"public","_id":"7196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"7255","relation":"source_file","date_created":"2020-01-12T11:49:49Z","date_updated":"2020-07-14T12:47:52Z","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","file_name":"thesis.zip","access_level":"closed","creator":"jtkadlec","content_type":"application/zip","file_size":21100497},{"file_id":"7367","relation":"main_file","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-28T07:32:42Z","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_name":"2020_Tkadlec_Thesis.pdf","access_level":"open_access","creator":"dernst","file_size":11670983,"content_type":"application/pdf"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"page":"144","citation":{"ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196."},"date_published":"2020-01-12T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"12","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publication_status":"published","year":"2020","date_created":"2019-12-20T12:26:36Z","date_updated":"2023-10-17T12:29:46Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7210"},{"id":"5751","status":"public","relation":"dissertation_contains"},{"id":"7212","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:52Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7196","publication_identifier":{"eissn":["2663-337X"]},"month":"01"},{"file_date_updated":"2021-03-02T15:38:14Z","author":[{"full_name":"Shevchenko, Alexander","last_name":"Shevchenko","first_name":"Alexander"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"}],"date_created":"2021-02-25T09:36:22Z","date_updated":"2023-10-17T12:43:19Z","volume":119,"acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","year":"2020","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"ML Research Press","month":"07","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1912.10095"]},"quality_controlled":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"abstract":[{"text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks.","lang":"eng"}],"type":"conference","file":[{"access_level":"open_access","file_name":"2020_PMLR_Shevchenko.pdf","creator":"dernst","file_size":5336380,"content_type":"application/pdf","file_id":"9217","relation":"main_file","success":1,"checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","date_updated":"2021-03-02T15:38:14Z","date_created":"2021-03-02T15:38:14Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9198","ddc":["000"],"status":"public","title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","intvolume":" 119","day":"13","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-07-13T00:00:00Z","publication":"Proceedings of the 37th International Conference on Machine Learning","citation":{"ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020."},"page":"8773-8784"},{"_id":"9157","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","title":"The weighted mean curvature derivative of a space-filling diagram","ddc":["510"],"status":"public","file":[{"checksum":"cea41de9937d07a3b927d71ee8b4e432","success":1,"date_updated":"2021-02-19T13:56:24Z","date_created":"2021-02-19T13:56:24Z","relation":"main_file","file_id":"9171","file_size":562359,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_CompMathBiophysics_Akopyan2.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"citation":{"ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100."},"publication":"Computational and Mathematical Biophysics","page":"51-67","article_type":"original","date_published":"2020-06-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","publisher":"De Gruyter","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"volume":8,"date_created":"2021-02-17T15:13:01Z","date_updated":"2023-10-17T12:34:51Z","ec_funded":1,"file_date_updated":"2021-02-19T13:56:24Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"quality_controlled":"1","doi":"10.1515/cmb-2020-0100","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2544-7297"]},"month":"06"},{"_id":"9156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","ddc":["510"],"status":"public","title":"The weighted Gaussian curvature derivative of a space-filling diagram","oa_version":"Published Version","file":[{"date_created":"2021-02-19T13:33:19Z","date_updated":"2021-02-19T13:33:19Z","success":1,"checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","relation":"main_file","creator":"dernst","file_size":707452,"content_type":"application/pdf","file_name":"2020_CompMathBiophysics_Akopyan.pdf","access_level":"open_access"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy."}],"citation":{"ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101."},"publication":"Computational and Mathematical Biophysics","page":"74-88","article_type":"original","date_published":"2020-07-21T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"21","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","publisher":"De Gruyter","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"volume":8,"date_created":"2021-02-17T15:12:44Z","date_updated":"2023-10-17T12:35:10Z","ec_funded":1,"file_date_updated":"2021-02-19T13:33:19Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.06777"]},"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1515/cmb-2020-0101","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2544-7297"]},"month":"07"},{"intvolume":" 25","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","status":"public","ddc":["510"],"_id":"8973","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_ElectronJProbab_Redig.pdf","creator":"dernst","content_type":"application/pdf","file_size":696653,"file_id":"8976","relation":"main_file","success":1,"checksum":"d75359b9814e78d57c0a481b7cde3751","date_updated":"2020-12-28T08:24:08Z","date_created":"2020-12-28T08:24:08Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"article_type":"original","citation":{"mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536"},"publication":"Electronic Journal of Probability","date_published":"2020-10-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"21","publisher":" Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"publication_status":"published","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","year":"2020","volume":25,"date_created":"2020-12-27T23:01:17Z","date_updated":"2023-10-17T12:51:56Z","author":[{"full_name":"Redig, Frank","first_name":"Frank","last_name":"Redig"},{"first_name":"Ellen","last_name":"Saada","full_name":"Saada, Ellen"},{"first_name":"Federico","last_name":"Sau","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"article_number":"138","ec_funded":1,"file_date_updated":"2020-12-28T08:24:08Z","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/20-EJP536","publication_identifier":{"eissn":["1083-6489"]},"month":"10"},{"year":"2020","department":[{"_id":"TiBr"}],"publisher":"Duke University Press","publication_status":"published","author":[{"full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","last_name":"Heath Brown","full_name":"Heath Brown, Roger"}],"volume":169,"date_created":"2018-12-11T11:45:02Z","date_updated":"2023-10-17T12:51:10Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"external_id":{"isi":["000582676300002"],"arxiv":["1805.10715"]},"isi":1,"quality_controlled":"1","doi":"10.1215/00127094-2020-0031","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"month":"09","_id":"179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 169","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","status":"public","oa_version":"Preprint","type":"journal_article","issue":"16","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"citation":{"ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” Duke Mathematical Journal, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","apa":"Browning, T. D., & Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2020-0031","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 2020;169(16):3099-3165. doi:10.1215/00127094-2020-0031","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal. Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031.","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165."},"publication":"Duke Mathematical Journal","page":"3099-3165","article_type":"original","date_published":"2020-09-10T00:00:00Z","article_processing_charge":"No","day":"10"},{"oa":1,"citation":{"ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","mla":"Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5973013.v1"}],"doi":"10.6084/m9.figshare.5973013.v1","date_published":"2020-10-15T00:00:00Z","article_processing_charge":"No","month":"10","day":"15","department":[{"_id":"KrCh"}],"publisher":"Royal Society","status":"public","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","_id":"9814","year":"2020","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-06T13:09:57Z","date_updated":"2023-10-18T06:36:00Z","related_material":{"record":[{"id":"198","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"type":"research_data_reference","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}]},{"article_number":"043202","volume":125,"date_created":"2020-08-24T06:24:04Z","date_updated":"2023-10-18T08:38:35Z","author":[{"last_name":"Malia","first_name":"Benjamin K.","full_name":"Malia, Benjamin K."},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"full_name":"Wu, Yunfan","last_name":"Wu","first_name":"Yunfan"},{"full_name":"Hosten, Onur","last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kasevich, Mark A.","first_name":"Mark A.","last_name":"Kasevich"}],"publisher":"American Physical Society","department":[{"_id":"OnHo"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.125.043202","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1912.10218","open_access":"1"}],"external_id":{"arxiv":["1912.10218"],"pmid":["32794788"],"isi":["000552227400008"]},"oa":1,"issue":"4","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 125","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8285","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2020-07-24T00:00:00Z","article_type":"original","citation":{"ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202."},"publication":"Physical Review Letters"},{"abstract":[{"text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient.","lang":"eng"}],"alternative_title":["OSA Technical Digest"],"article_number":"QTu8A.1","type":"conference","date_created":"2021-11-21T23:01:31Z","date_updated":"2023-10-18T08:32:34Z","oa_version":"None","author":[{"last_name":"Lambert","first_name":"Nicholas J.","full_name":"Lambert, Nicholas J."},{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"publication_status":"published","status":"public","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","department":[{"_id":"JoFi"}],"publisher":"Optica Publishing Group","_id":"10328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","month":"01","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"scopus_import":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2020-09-17","start_date":"2020-09-14","location":"Washington, DC, United States","name":"OSA: Optical Society of America"},"date_published":"2020-01-01T00:00:00Z","doi":"10.1364/QUANTUM.2020.QTu8A.1","quality_controlled":"1","publication":"OSA Quantum 2.0 Conference","citation":{"mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1"}},{"acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","year":"2020","publication_status":"published","department":[{"_id":"TiVo"}],"author":[{"full_name":"Confavreux, Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux","first_name":"Basile J"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"},{"full_name":"Agnes, Everton J.","first_name":"Everton J.","last_name":"Agnes"},{"full_name":"Lillicrap, Timothy","last_name":"Lillicrap","first_name":"Timothy"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P"}],"related_material":{"link":[{"relation":"is_continued_by","url":"https://doi.org/10.1101/2020.10.24.353409"}],"record":[{"id":"14422","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-10-18T09:20:55Z","date_created":"2021-07-04T22:01:27Z","volume":33,"ec_funded":1,"oa":1,"main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."},{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2020-12-12","start_date":"2020-12-06","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["1049-5258"]},"_id":"9633","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","status":"public","intvolume":" 33","oa_version":"Published Version","type":"conference","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"publication":"Advances in Neural Information Processing Systems","citation":{"ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408."},"page":"16398-16408","date_published":"2020-12-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No"},{"publication":"Cell Reports","citation":{"apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020.","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463."},"article_type":"original","date_published":"2020-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8943","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","ddc":["580"],"status":"public","intvolume":" 33","file":[{"creator":"dernst","content_type":"application/pdf","file_size":8056434,"file_name":"2020_CellReports_Tan.pdf","access_level":"open_access","date_updated":"2020-12-14T07:33:39Z","date_created":"2020-12-14T07:33:39Z","success":1,"checksum":"ed18cba0fb48ed2e789381a54cc21904","file_id":"8948","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000595658100018"],"pmid":["33264621"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"doi":"10.1016/j.celrep.2020.108463","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"eissn":["22111247"]},"year":"2020","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"author":[{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Di Donato, Martin","last_name":"Di Donato","first_name":"Martin"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi"},{"full_name":"Klíma, Petr","last_name":"Klíma","first_name":"Petr"},{"full_name":"Liu, Jie","first_name":"Jie","last_name":"Liu"},{"first_name":"Aurélien","last_name":"Bailly","full_name":"Bailly, Aurélien"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plants-on-aspirin/"}]},"date_created":"2020-12-13T23:01:21Z","date_updated":"2023-11-16T13:03:31Z","volume":33,"article_number":"108463","file_date_updated":"2020-12-14T07:33:39Z","ec_funded":1},{"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.11190"}],"oa":1,"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"project":[{"grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1913716117","language":[{"iso":"eng"}],"ec_funded":1,"year":"2020","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"relation":"dissertation_contains","status":"public","id":"14530"}]},"author":[{"id":"3454D55E-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Duo","full_name":"Xu, Duo"},{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0179-9737","first_name":"Xingyu","last_name":"Ma","full_name":"Ma, Xingyu"},{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"volume":117,"date_created":"2020-06-07T22:00:51Z","date_updated":"2023-11-30T10:55:13Z","scopus_import":"1","article_processing_charge":"No","day":"26","citation":{"chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"11233-11239","article_type":"original","date_published":"2020-05-26T00:00:00Z","type":"journal_article","issue":"21","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7932","intvolume":" 117","status":"public","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","oa_version":"Preprint"},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["General Mathematics"],"date_published":"2020-09-01T00:00:00Z","article_type":"original","page":"1421-1539","publication":"Documenta Mathematica","citation":{"ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539."},"abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1374708,"content_type":"application/pdf","file_name":"2020_DocumentaMathematica_Alt.pdf","access_level":"open_access","date_created":"2023-12-18T10:42:32Z","date_updated":"2023-12-18T10:42:32Z","success":1,"checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","file_id":"14695","relation":"main_file"}],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","status":"public","ddc":["510"],"intvolume":" 25","_id":"14694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"language":[{"iso":"eng"}],"doi":"10.4171/dm/780","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1804.07752"]},"file_date_updated":"2023-12-18T10:42:32Z","date_updated":"2023-12-18T10:46:09Z","date_created":"2023-12-18T10:37:43Z","volume":25,"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6183"}]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"EMS Press","year":"2020"},{"publication_identifier":{"issn":["2663-337X"]},"month":"07","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8156","oa":1,"file_date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-23T09:51:29Z","date_updated":"2023-12-18T10:51:01Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8182"},{"relation":"part_of_dissertation","status":"public","id":"8183"},{"status":"public","relation":"part_of_dissertation","id":"8185"},{"id":"8184","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6355"},{"status":"public","relation":"part_of_dissertation","id":"75"}]},"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2020","article_processing_charge":"No","has_accepted_license":"1","day":"24","date_published":"2020-07-24T00:00:00Z","page":"119","citation":{"ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156."},"abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"8178","date_updated":"2020-07-27T12:44:51Z","date_created":"2020-07-27T12:44:51Z","file_name":"source.zip","access_level":"closed","content_type":"application/zip","file_size":1061740,"creator":"savvakum"},{"file_id":"8179","relation":"main_file","success":1,"date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-27T12:46:53Z","access_level":"open_access","file_name":"thesis_pdfa.pdf","creator":"savvakum","file_size":1336501,"content_type":"application/pdf"}],"oa_version":"Published Version","title":"Topological methods in geometry and discrete mathematics","status":"public","ddc":["514"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8156"},{"month":"01","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1903.04046","open_access":"1"}],"external_id":{"arxiv":["1903.04046"]},"language":[{"iso":"eng"}],"doi":"10.2140/paa.2020.2.35","publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"RoSe"}],"year":"2020","date_created":"2024-01-28T23:01:44Z","date_updated":"2024-01-29T09:01:12Z","volume":2,"author":[{"full_name":"Lewin, Mathieu","first_name":"Mathieu","last_name":"Lewin"},{"full_name":"Lieb, Elliott H.","last_name":"Lieb","first_name":"Elliott H."},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"35-73","publication":"Pure and Applied Analysis","citation":{"chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/paa.2020.2.35.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2020). The local density approximation in density functional theory. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2020.2.35","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation in density functional theory,” Pure and Applied Analysis, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020.","ista":"Lewin M, Lieb EH, Seiringer R. 2020. The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","ama":"Lewin M, Lieb EH, Seiringer R. The local density approximation in density functional theory. Pure and Applied Analysis. 2020;2(1):35-73. doi:10.2140/paa.2020.2.35"},"date_published":"2020-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space.","lang":"eng"}],"issue":"1","title":" The local density approximation in density functional theory","status":"public","intvolume":" 2","_id":"14891","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"publisher":"Elsevier","department":[{"_id":"LoSw"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. 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Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"page":"81-95","article_type":"original","citation":{"ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 2020;450:81-95. doi:10.1016/j.neuroscience.2020.08.011","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 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Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data","date_published":"2020-12-02T00:00:00Z","doi":"10.15479/AT:ISTA:8834","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834.","short":"G. Katsaros, (2020).","mla":"Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8834.","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834."},"month":"12","day":"02","article_processing_charge":"No","has_accepted_license":"1"},{"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"day":"15","month":"07","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097.","short":"B. Kavcic, (2020).","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:8097","date_published":"2020-07-15T00:00:00Z","type":"research_data","file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology.","lang":"eng"}],"status":"public","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8097","year":"2020","date_created":"2020-07-06T20:40:19Z","date_updated":"2024-02-21T12:40:51Z","file":[{"relation":"main_file","file_id":"8098","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","date_created":"2020-07-06T20:38:27Z","date_updated":"2020-07-14T12:48:09Z","access_level":"open_access","file_name":"natComm_2020_scripts.zip","file_size":255770756,"content_type":"application/zip","creator":"bkavcic"}],"oa_version":"Published Version","author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","contributor_type":"research_group","last_name":"Tkačik"},{"first_name":"Tobias","contributor_type":"research_group","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}]},{"type":"research_data","file_date_updated":"2020-08-18T08:03:23Z","abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"ddc":["576"],"status":"public","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8254","year":"2020","date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","oa_version":"Published Version","file":[{"date_created":"2020-08-18T08:03:23Z","date_updated":"2020-08-18T08:03:23Z","success":1,"checksum":"4f1382ed4384751b6013398c11557bf6","file_id":"8280","relation":"main_file","creator":"dernst","file_size":5778420,"content_type":"application/x-zip-compressed","file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access"}],"author":[{"full_name":"Arathoon, Louise S","last_name":"Arathoon","first_name":"Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11321","relation":"later_version","status":"public"},{"status":"public","relation":"later_version","id":"9192"}]},"contributor":[{"contributor_type":"data_collector","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Surendranadh","contributor_type":"project_member","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","last_name":"Barton","contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","last_name":"Field"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","contributor_type":"project_member","first_name":"Melinda"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","contributor_type":"project_member"}],"month":"08","day":"18","article_processing_charge":"No","has_accepted_license":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254.","short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254."},"date_published":"2020-08-18T00:00:00Z","doi":"10.15479/AT:ISTA:8254"},{"date_published":"2020-04-23T00:00:00Z","citation":{"mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523.","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020."},"publication":"Advanced Materials","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"23","scopus_import":"1","file":[{"file_id":"8782","relation":"main_file","success":1,"checksum":"c622737dc295972065782558337124a2","date_updated":"2020-11-20T10:11:35Z","date_created":"2020-11-20T10:11:35Z","access_level":"open_access","file_name":"2020_AdvancedMaterials_Gao.pdf","creator":"dernst","content_type":"application/pdf","file_size":5242880}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7541","intvolume":" 32","status":"public","title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","ddc":["530"],"issue":"16","abstract":[{"lang":"eng","text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon."}],"type":"journal_article","doi":"10.1002/adma.201906523","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000516660900001"]},"oa":1,"project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0935-9648"]},"month":"04","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7996"},{"id":"9222","status":"public","relation":"research_data"}]},"author":[{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"last_name":"Wang","first_name":"Jian-Huan","full_name":"Wang, Jian-Huan"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes"},{"last_name":"Hu","first_name":"Hao","full_name":"Hu, Hao"},{"full_name":"Rančić, Marko J.","last_name":"Rančić","first_name":"Marko J."},{"first_name":"Jie-Yin","last_name":"Zhang","full_name":"Zhang, Jie-Yin"},{"full_name":"Wang, Ting","first_name":"Ting","last_name":"Wang"},{"first_name":"Yuan","last_name":"Yao","full_name":"Yao, Yuan"},{"full_name":"Wang, Gui-Lei","last_name":"Wang","first_name":"Gui-Lei"},{"last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"full_name":"Vukušić, Lada","first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636"},{"first_name":"Christoph","last_name":"Kloeffel","full_name":"Kloeffel, Christoph"},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"full_name":"Liu, Feng","first_name":"Feng","last_name":"Liu"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"}],"volume":32,"date_updated":"2024-02-21T12:42:12Z","date_created":"2020-02-28T09:47:00Z","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","year":"2020","department":[{"_id":"GeKa"}],"publisher":"Wiley","publication_status":"published","ec_funded":1,"file_date_updated":"2020-11-20T10:11:35Z","article_number":"1906523"},{"file_date_updated":"2020-12-09T15:00:19Z","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"type":"research_data","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","full_name":"Kavcic, Bor"}],"contributor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","last_name":"Tkačik","first_name":"Gašper"},{"contributor_type":"supervisor","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8997","relation":"used_in_publication","status":"public"}]},"date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","file":[{"file_id":"8932","relation":"main_file","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","access_level":"open_access","file_name":"PLoSCompBiol2020_datarep.zip","creator":"bkavcic","file_size":315494370,"content_type":"application/zip"}],"oa_version":"Published Version","year":"2020","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","ddc":["570"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"month":"12","day":"10","article_processing_charge":"No","has_accepted_license":"1","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"doi":"10.15479/AT:ISTA:8930","date_published":"2020-12-10T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020."}},{"type":"research_data","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"file_date_updated":"2020-12-20T22:01:44Z","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","status":"public","ddc":["570"],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","_id":"8951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","date_updated":"2024-02-21T12:41:57Z","date_created":"2020-12-20T10:00:26Z","file":[{"file_name":"readme.txt","access_level":"open_access","creator":"bkavcic","content_type":"text/plain","file_size":523,"file_id":"8952","relation":"main_file","date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1"},{"access_level":"open_access","file_name":"GRNs Research depository.gb","creator":"bkavcic","content_type":"application/octet-stream","file_size":379228,"file_id":"8954","relation":"main_file","success":1,"checksum":"f2c6d5232ec6d551b6993991e8689e9f","date_updated":"2020-12-20T22:01:44Z","date_created":"2020-12-20T22:01:44Z"}],"oa_version":"Published Version","author":[{"full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","first_name":"Anna A","last_name":"Nagy-Staron"}],"contributor":[{"first_name":"Anna A","last_name":"Nagy-Staron","contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","contributor_type":"project_member","last_name":"Tomasek"},{"last_name":"Caruso Carter","contributor_type":"project_member","first_name":"Caroline"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"first_name":"Bor","last_name":"Kavcic","contributor_type":"project_member","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"contributor_type":"project_member","last_name":"Paixão","first_name":"Tiago"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","contributor_type":"project_manager"}],"related_material":{"record":[{"id":"9283","status":"public","relation":"used_in_publication"}]},"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"month":"12","day":"21","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020)."},"oa":1,"doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z"},{"article_processing_charge":"No","has_accepted_license":"1","day":"28","month":"01","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"doi":"10.15479/AT:ISTA:7383","date_published":"2020-01-28T00:00:00Z","citation":{"apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383."},"oa":1,"file_date_updated":"2020-07-14T12:47:57Z","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"type":"research_data","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Scripts.zip","content_type":"application/zip","file_size":73363365,"creator":"rgrah","relation":"main_file","file_id":"7384","checksum":"9d292cf5207b3829225f44c044cdb3fd","date_created":"2020-01-28T10:39:40Z","date_updated":"2020-07-14T12:47:57Z"},{"checksum":"4076ceab32ef588cc233802bab24c1ab","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:30Z","relation":"main_file","file_id":"7385","file_size":962,"content_type":"text/plain","creator":"rgrah","access_level":"open_access","file_name":"READ_ME_MAIN.txt"}],"date_created":"2020-01-28T10:41:49Z","date_updated":"2024-02-21T12:42:31Z","contributor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C"}],"related_material":{"record":[{"id":"7652","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","year":"2020","_id":"7383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222","chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","short":"G. Katsaros, (2020)."},"oa":1,"doi":"10.15479/AT:ISTA:9222","date_published":"2020-03-16T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","month":"03","day":"16","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["530"],"title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","year":"2020","_id":"9222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2021-03-05T17:50:45Z","date_created":"2021-03-05T17:50:45Z","checksum":"41b66e195ed3dbd73077feee77b05652","relation":"main_file","file_id":"9223","file_size":13317557,"content_type":"application/x-zip-compressed","creator":"gkatsaro","file_name":"DOI_SiteControlledHWs.zip","access_level":"open_access"},{"relation":"main_file","file_id":"9233","date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","success":1,"file_name":"Readme.txt","access_level":"open_access","file_size":3515,"content_type":"text/plain","creator":"dernst"}],"date_updated":"2024-02-21T12:42:13Z","date_created":"2021-03-05T18:00:47Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7541"}]},"contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","contributor_type":"research_group","last_name":"Katsaros","first_name":"Georgios"}],"author":[{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z"},{"month":"09","publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8366","file_date_updated":"2020-09-16T15:11:01Z","ec_funded":1,"publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","year":"2020","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","date_created":"2020-09-10T16:19:55Z","date_updated":"2024-02-21T12:44:29Z","author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"7151","relation":"research_data","status":"deleted"},{"id":"7262","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8562"},{"status":"public","relation":"part_of_dissertation","id":"1001"},{"id":"8375","relation":"research_data","status":"public"}]},"keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"day":"21","article_processing_charge":"No","has_accepted_license":"1","page":"118","citation":{"ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366."},"date_published":"2020-09-21T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop.","lang":"eng"}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","ddc":["000"],"status":"public","_id":"8366","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"rguseino","content_type":"application/pdf","file_size":70950442,"access_level":"open_access","file_name":"thesis_rguseinov.pdf","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","date_created":"2020-09-10T16:11:49Z","date_updated":"2020-09-10T16:11:49Z","file_id":"8367","relation":"main_file"},{"content_type":"application/x-zip-compressed","file_size":76207597,"creator":"rguseino","file_name":"thesis_source.zip","access_level":"closed","date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-11T09:39:48Z","checksum":"e8fd944c960c20e0e27e6548af69121d","relation":"source_file","file_id":"8374"}]},{"date_published":"2020-11-26T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843","ieee":"K. Gavriil et al., “Computational design of cold bent glass façades,” ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing Machinery, 2020.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:10.1145/3414685.3417843.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843."},"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"13084","checksum":"c7f67717ad74e670b7daeae732abe151","success":1,"date_updated":"2023-05-23T20:54:43Z","date_created":"2023-05-23T20:54:43Z","access_level":"open_access","file_name":"coldglass.pdf","file_size":28964641,"content_type":"application/pdf","creator":"bbickel"}],"status":"public","ddc":["000"],"title":"Computational design of cold bent glass façades","intvolume":" 39","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8562","abstract":[{"lang":"eng","text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface."}],"issue":"6","type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3414685.3417843","quality_controlled":"1","isi":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2009.03667"],"isi":["000595589100048"]},"oa":1,"month":"11","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"date_created":"2020-09-23T11:30:02Z","date_updated":"2024-02-21T12:43:21Z","volume":39,"author":[{"first_name":"Konstantinos","last_name":"Gavriil","full_name":"Gavriil, Konstantinos"},{"last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus"},{"first_name":"Davide","last_name":"Pellis","full_name":"Pellis, Davide"},{"first_name":"Paul M","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M"},{"full_name":"Rist, Florian","first_name":"Florian","last_name":"Rist"},{"full_name":"Pottmann, Helmut","last_name":"Pottmann","first_name":"Helmut"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/bend-dont-break/"}],"record":[{"id":"8366","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"8761"}]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"year":"2020","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","file_date_updated":"2023-05-23T20:54:43Z","ec_funded":1,"article_number":"208"},{"related_material":{"record":[{"id":"7689","status":"public","relation":"research_data"}]},"author":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip"},{"full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukušić"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"orcid":"0000-0002-4619-9575","last_name":"Wang","first_name":"Ting","full_name":"Wang, Ting"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"first_name":"Karsten","last_name":"Held","full_name":"Held, Karsten"}],"volume":20,"date_updated":"2024-02-21T12:44:01Z","date_created":"2020-08-06T09:25:04Z","pmid":1,"acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","year":"2020","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-08-06T09:35:37Z","doi":"10.1021/acs.nanolett.0c01466","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"project":[{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"06","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_NanoLetters_Katsaros.pdf","content_type":"application/pdf","file_size":3308906,"creator":"dernst","relation":"main_file","file_id":"8204","success":1,"date_created":"2020-08-06T09:35:37Z","date_updated":"2020-08-06T09:35:37Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8203","intvolume":" 20","status":"public","ddc":["530"],"title":"Zero field splitting of heavy-hole states in quantum dots","issue":"7","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"type":"journal_article","date_published":"2020-06-01T00:00:00Z","citation":{"ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466","ieee":"G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01466.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:10.1021/acs.nanolett.0c01466.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206."},"publication":"Nano Letters","page":"5201-5206","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1"},{"file":[{"file_name":"2020_eLife_Gridchyn.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":447669,"file_id":"8749","relation":"main_file","date_created":"2020-11-09T09:17:40Z","date_updated":"2020-11-09T09:17:40Z","success":1,"checksum":"6a7b0543c440f4c000a1864e69377d95"}],"oa_version":"Published Version","intvolume":" 9","title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","status":"public","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8740","abstract":[{"lang":"eng","text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells."}],"type":"journal_article","date_published":"2020-10-05T00:00:00Z","article_type":"original","citation":{"ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.61106","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 9, 61106.","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 2020;9. doi:10.7554/eLife.61106","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.61106.","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, ELife 9 (2020).","mla":"Gridchyn, Igor, et al. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife, vol. 9, 61106, eLife Sciences Publications, 2020, doi:10.7554/eLife.61106."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"05","scopus_import":"1","volume":9,"date_updated":"2024-02-21T12:43:40Z","date_created":"2020-11-08T23:01:25Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"8563"}]},"author":[{"id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor"},{"full_name":"Schönenberger, Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp"},{"last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"department":[{"_id":"JoCs"}],"publisher":"eLife Sciences Publications","publication_status":"published","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","year":"2020","file_date_updated":"2020-11-09T09:17:40Z","article_number":"61106","language":[{"iso":"eng"}],"doi":"10.7554/eLife.61106","project":[{"call_identifier":"FWF","name":"Interneuron plasticity during spatial learning","grant_number":"I2072-B27","_id":"257D4372-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Interneuro Plasticity During Spatial Learning","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000584369000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["2050084X"]},"month":"10"}]